I’ve not tried MBR1… but: you can indeed boot Windows 7 and Windows 8 (64-bit versions) in EFI mode off of a Thunderbolt-connected disk. I have a handful of the Buffalo Ministation Thunderbolt2 drives with the original, slow 5400 rpm hard drives replaced with various SSDs, and they work wonderfully3. You can boot off of them by pressing Option during the chime at bootup, and they show as an orange-colored "EFI Disk" in the selection options.
Now, the trick is getting Windows installed on the disk in EFI mode, because when you stated that "the EFI version of Windows doesn't seem to be compatible with Apple's EFI implementation," I assume that means (like me), you tried, and it just refused to install. Well, to my knowledge, that's correct — however, the only part that isn't 'compatible' is the install process — whatever Windows tries to do to the EFI partition just before it goes to reboot doesn't work out right.
Solution to the rescue: install VMware Fusion on your Mac (even the trial will do) and use Vijay Pandurangan’s blog post to help you mount your external Thunderbolt drive directly to a new VM. Pay special attention to the comment at the bottom of the post: Hajo makes it much, much easier.
Partition the drive as GPT with OS X, and/or install an extra copy of OS X on the Thunderbolt disk first (if you wish) and leave free space for Windows. If you’re not planning to have a spare copy of OS X to boot from this drive, leave all the space blank (don’t partition beyond the EFI partition OS X will initialize with GPT).
Set the VM to boot with EFI, and install Windows 7 or Windows 8 (has to be a 64-bit flavor to support EFI) directly to the disk. Now, once Windows has gone through its setup process, and it counts down for a restart, shut the VM down. That’s right - you're done with Fusion4,5, and you can go straight to booting from your new drive. Seriously. Press Option on boot, and you will indeed see "EFI Boot" as an option, you can choose it, and Windows on Thunderbolt you will have.
I don't expect you would have any issue booting from any other standard Thunderbolt drive either, especially if it is an AHCI SATA drive like the Buffalo.
While I’m fairly confident that you could get plain-old MBR-based Boot Camp to work, why would you? EFI is the future, and once you go through the process, you can boot your Thunderbolt Windows disk from just about any new Mac5.
1 I haven't had the need for it, yet. There isn't an OS, or utility I've needed to run on my Macs that doesn't have EFI support, and I have an aversion to looking back and strongly feel MBR is looking back — like 1983 called, and wants its 10MB MFM hard drive back, back.
2 The original disk worked fine too, but gaaah! so sloooww.
3 Brian Klug wrote a really excellent review on this particular drive on AnandTech, and that's what convinced me to buy it. It's a beautiful piece of equipment, with fit-and-finish like Apple, comes with both a Thunderbolt and USB 3 connector and cables! to match. Yes, the included drive is slow as all get out, but you can replace it with just about any 2.5" HDD or SSD of your choosing. Just make sure you have a hair dryer.
4 Unless, you're not. I use both interchangeably. You can boot directly into Windows 8 on hardware, and you can boot into it from Fusion using this configuration when the need strikes you, like you're working on something, don’t want to reboot, but need to open a .PST file in Outlook 2013… for instance.
5 Windows licensing issues notwithstanding; you’re going to have to buy a copy of Windows for every machine you want to boot it on for long-term use in order to not get black backgrounds and "this copy is not genuine" type errors.
This might seem like a long shot, but it was also the only option for me to install Windows into my Bootcamp partition a little while back.
It's also the only option for a Mac that used to have an optical drive but no longer does, since for some reason these devices are no longer able to boot from USB.
- Use Disk Utility to create a FAT partition a little larger than your wanted Windows partition.
- Install rEFIt.
- Reboot twice for rEFIt to install properly. As soon as you see the rEFIt boot menu when starting, it's good. Here you choose the 'Partition Tool', with which you'll change the MBR (Master Boot Record). (On a side note: You can easily uninstall rEFIt by renaming the directory at the root of your harddrive)
- Install VirtualBox, Parallels or VMware. I did this with VMware back at the time, but all of these should work as long as you're able to mount the virtual harddrive like any removable disk.
- Use the virtualization software to install Windows into a virtual machine at the size of your wanted partition (not what you made it above, but a little smaller than that). You can of course install from an ISO here, making the state of your disc drive irrelevant. Kill the virtual machine as soon as it reboots the first time after finishing the installation, stopping Windows before being able to configure itself.
- Use the virtualization software's features to mount the virtual harddrive.
- Install a tool called WinClone.
- If your virtual drive is mounted, WinClone should be able to see this in the tab 'Image'. Pull this into an image onto your harddrive.
- Now choose the 'Restore' tab in WinClone and restore this image to your Bootcamp partition.
- Now you can reboot and boot into your Bootcamp partition with rEFIt, which is no longer of any use from this point on, but you can keep it around as well. Windows should now continue configuring itself and finish the installation.
I stumbled across this solution here in the Apple Support Community and posted about it here a while ago on a German Apple User Forum, if that turns out to be of any use to anybody.
Best Answer
Below is a quote taken from the Boot Camp Installation & Setup Guide (copyright 2013).
So, it is possible to install Windows via Boot Camp, on a drive that is not the main drive. The maximum Windows that Apple officially supports is Windows 8.1 (64-Bit). Microsoft says you should be able to upgrade an existing Boot Camp Windows 8.1 installation to Windows 10.
Everything I have posted so far is by the book. However, you are proposing going off script by directly installing Windows 10. Officially, the answer is no, but unofficially the answer probably is yes. If you try, expect to encounter Scarecrows. In other words, expect error messages from Apple as some point during the installation that will say you can not proceed. There is usually are one or more ways to bypass any problems that you will encounter. You can try posting a problem here and see if anyone can suggest a solution.
Here is some advice.
There is always the possibility that Windows 10 is not compatible with your processor. I assume the Windows 10 installer would inform you, if this was the case. I have encountered PCs where I could install 64 bit Windows 7, 8 and 8.1, but not Windows 10. Basically, the processor did not meet the requirements given below. (This was taken from the Microsoft web site: Minimum hardware requirements, Section 3.1 Processor)
On the other hand, I came across the Microsoft website: Windows Processor Requirements, which states:
Apparently, you can download and try Windows 10 Enterprise for free. See the Microsoft Evaluation Center website.
If you do not use the Boot Camp Assistant to install Widows, then you should follow the instructions provided by Microsoft. For BIOS booting Windows, the instructions for partitioning can be found at the BIOS/MBR-based hard drive partitions website.
I would recommend placing the System partition on the first (main) drive and then placing the Windows and Recovery partitions on a second internal drive. You could combine the Windows and Recovery partitions, if you wish. This System partition is only appropriately 100 MB in size, so the partition should have minimum impact on the space for macOS.