Wierd -I'm running a somewhat elderly version (Dec 2000) of the TIS, which only covers the E46 M3 up to 2001, largely prior to it's USA debut. There is no such disclaimer on my version.
But back checking to the E36 M3, it is exactly there where you said it would be - "(M models may not be machined)"
So the two questions are -
(1) did the non-machining direction get included for the E46 M3 in a later version of the TIS?
(2) Why not? As noted above, my first guess would be that the real issue is the compound floating rotor design prevents accurate machining, but are there other considerations? And for that matter, did the E36 even use that design?
As I recall the thread you're refering to, I believe the conclusion was, yes you can machine the rotors, but it's to imagine the circumstances where it would be worth the bother (and expense).