REAPER supports up to 64ch so it's possible for FFTMT to have an elegant design to work on 4ch directly (dual stereo). So you need only 2 tracks to work it.
If your DAW only supports stereo/2ch, You can already do this with kn0ckout VST but you need 6 tracks with complex & awkward routing. SO there's no way to use FFTMT subtract & we're back to square 1.
You can load the JS/txt with https://www.reaper.fm/reaplugs/ VST on windows & set the appropriate options for FFTMT subtract if your DAW supports at least 4ch (or 5.1 surround) & flexible routing. The idea is this: send the instro to ch3-4 of the full mix, and use FFTMT to subtract.