If I recall correctly, it's not so much an issue of actual filesystem incompatibilities, but rather something to do with Windows not respecting the other bootloader well. Separate drives mitigate that issue.
I haven't tried dual-booting since I moved to Windows 7 (on 10 now), but I never had any issues whatsoever as long as you installed Windows first and then whatever other OS after.
Windows only clobbers the MBR during install in my experience.
You boot on one disk or the other, I think (I never did that, but a classmate did)