Makes sense.
Brainstorming some more, I did find that I can override the isWindows classification despite them telling me I can't. Turns out if you make your own isWindows AppliesTo function, that overrides the built-in one. I did a quick test with this logic and it seemed to do what I needed. See any issues with this (other than it not being officially supported)?
(join(system.categories,",") =~ "Windows" || join(system.categories,",") =~ "Hyper-V" || system.sysinfo =~ "Windows" || system.sysinfo =~ "Hyper-V")
&& !hasCategory("Crestron")
(we are applying the Crestron category as needed)
