Is there a way to make an iMac's internal drive disappear completely WITHOUT removing it?
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?