MacOS – Buzzing sound on Macbook Pro mid 2012 due to optical drive fixed

Since only one drive gives you a flashing ? when mounted internally, you've pretty much ruled out hardware failure of the controller and the cabling.

I would first try booting into the start up manager by holding the option key with the problematic drive on the internal bus. The ? can come up when the startup disk settings in NVRAM don't match the drive, but if any drive connected is bootable, it should show when you boot with option held down.

Your next step after making sure it's not startup disk settings would be to erase that drive entirely and try reinstalling OS X onto it. You could flip a coin and decide to do the installation internally or externally.

I believe the issue to be that the controller is still SATA III for the optical bay, yet the connector is a SATA II type, as is the cable. So if you try and place a SATA III enabled drive in the optical bay, it will try and negotiate at SATA III speed (6G). This creates an issue as the cable is not setup for this and the crosstalk, and very low SNR at that speed causes many errors. I got my Seagate Momentus SSHD disk drive working somewhat in the optical bay by wrapping it and the short cable in tin foil, making it a good ground to the chassis, but it still had loads of errors on it. I ended up putting a SATA II disk in which works. My Macbook is a 2012 13in with an 2.9GHz i7 in it. This shows both connectors as 7 series Intel Chipset, both of them are supported for 6G, yet the optical drive is negotiated as 3G (SATA II). My Samsung SSD in the HDD bay, is negotiated as the full 6G.

Have a check in system profiler to see what supported speeds and negotiated speeds you are seeing for your controllers. There seems to be a lot of conflicting information about what model supports what, but it makes sense that the controllers are the same type on the main board for the particular chipset being used. The connectors are different though.

I was hoping there would be a hard disk that you can force SATA II on, or some way of enforcing the controller to only ever negotiate up to 3G, but thus far haven't had any luck :-(

Hope that helps demystify the core issue at stake here somewhat.