Vampire is not very compatible no. Lots of things break as their priority is writing new apps and tools and not legacy compatibility. This is a problem going forward. Its too bad as its a cool and innovative project. But for some reason they leaders want to create some new OS for vampire.
Why almost everything works on my vamp then ? i think it's very compatible backwards wise.
Also do not forget 68080 is a MUCH more modern/advanced beast then 68060.
All system/OS friendly software just works that's it.
I got my own hand build OS3.9 install (and yes i have a legal original copy of OS3.9) installed almost every hack/patch and add-on known to Amiga kind and it runs rock solid.
To put in another perspective the old PPC cards where not compatible, because you needed WarpOS and specially written software to make use of PPC.
With the FPU now shaping up, Vampire is gaining more compatibility again.
My point is that with going forward you will always loose some compatibility and must find workarounds to regain backwards compatibility, but in this case it's very very little, heck you dont even need the 68040.library anymore.
Until WHDload you could not play any or almost none of the old games for A500 on 040 and 060, to have WHDload tuned in for vamp will take time.
The only thing i cannot run ATM is AGA software because it's not implemented yet.
Sure when writing new apps that take full advantage of apollo-core features will not run on older 68K CPU's, but it makes software possible that would never run anywhere decent on 040 and 060 (like playing mpeg on 640x360@24 or 30 fps consistent) or run Netsurf usable.
And to put in further perspective probably there are now more active vampire users then 060 users, if not then it will be in the very near future.