Debian Filesystems – How to Find Out About Rootfs

First and foremost, this is going to depend solely on your architecture, and customs.

I for instance mount things like this under /mnt. I know people that create top level directories, and people who put this stuff in /home. It all depends on what you're comfortable with. There is no distinct standard on this anymore, the architecture of the system has changed, and you have varying views now, on things that used to be 'gospel'. Things like /usr/local or /opt/share, rpm or source...you get the drift.

Secondly, if you re-read through your link at pathname.com, you'll notice the paragraph under /media that states

Rationale

Historically there have been a number of other different places used to mount removeable media such as /cdrom, /mnt or /mnt/cdrom. Placing the mount points for all removeable media directly in the root directory would potentially result in a large number of extra directories in /. Although the use of subdirectories in /mnt as a mount point has recently been common, it conflicts with a much older tradition of using /mnt directly as a temporary mount point.

So personally, I advocate /mnt/windows or some iteration of that. It keeps the top level dir free, and is simple and intuitive. When I'm looking through or auditing a system, that's where I look for mounts right off the bat.

The issue turned out to be unrelated to LVM. As clarified in Why does this change render my Block Device unbootable?, the real issue is that by separating / and /boot into two separate partitions, the MBR configuration was no longer correct. I was unable to update GRUB configuration files to fix this, so ultimately I had to keep / and /boot on the same partition and add my other partitions separately. Not ideal but it works.