Is there a way to make an iMac's internal drive disappear completely WITHOUT removing it? I want to make it so that it can't be seen or written to while booted from an external drive.

For some background, I use a cross-platform dev environment that can target Linux and want to install the recommended Linux distro for testing. Every time I've tried before, it wrote a boot loader to the internal drive that must be messed up because my Bootcamped Win 10 won't boot afterwards. If it matters the req'd distro is Linux Mint Cinnamon Edition.
You appear to have two questions/issues:

1) A Linux system has "boot jacked" your boot manager/boot loader, messing up Windows.

2) Hiding above system from macOS.

You could give rEFInd a try to fix/manage your boot issues.  It should solve 1 but not 2 per se.

There may be a solution for 2 here:
How to prevent auto mounting of a volume in macOS High Sierra?