Does/might the added crap throw off timings and functionalities of current 680x0, or is it cause its an unknown variable as to how a routine will actually run?
The timing is off on purpose, which is forgivable, but you could end up writing code that only runs on the 68080 but fails on the 68060 because of race conditions (and vice versa). This can happen on real cpus as well, but the hostility from 68080 supporters indicates that a lot of people don't care if software only runs on 68080 and not 68060. So don't expect anything to work.
Any software taking advantage of the "added crap" can't run on current 680x0 in any case, again the hostility from 68080 supporters indicates they don't care.
Meanwhile anyone writing software that uses 680x0 features that aren't supported by 68080 gets hostility if they request it.
You can't put the 68080 into a nextcube or 68k mac. That doesn't seem to be something that apollo cares about, it's not really 68040/68060 compatible (next and mac require 68040 and won't work with 68060). They would be even better demos of their core, if only they'd support the FPU and MMU (it has been suggested that peoples requests for it are the reason why it hasn't been worked on, which is kinda weird).