Does AROS have an integrated UAE type emulation layer like MorphOS or Amithlon?
No.
In fact the two similar options you present are different already:
MorphOS - no chipset emulation, custom powerpc JIT, 68k apps run inside the powerpc OS, taking advantage of the native OS routines, 68k apps are just like any other applications. 68k apps have access to the native system resources such as 3d acceleration. MorphOS 68k emulation has nothing to do with UAE.
Amithlon - stripped down UAE sitting on top of linux kernel, has a fast JIT engine AFAIK only partially based on the UAE one, limited HW emulation, there is a way to call native x86 routines. 68k apps have access to the bare HW here as well.
As far as I know AROS is opting for UAE integration: Running a stock UAE, sharing clipboard, filesystems etc. Much like what you have with VMWare where you can access the host system resources (note: vmware is used here only as a reference to how the host environment can be accessed).
The obvious plus here is that it will run pretty much anything UAE does. Downside is that it will be a pain to integrate it anywhere near as good as MorphOS or Amithlon. For instance it will be hard to make the 68k apps not look out of place (Preferences are hard to propagate etc). The biggest problem probably is that it requires a legal copy of the AmigaOS to be able to run anything (There have been talks about using AROS 68k as a AmigaOS replacement, but as far as I can tell that plan hasn't advanced).
Speaking of which, is there "Unity" mode in the AROS UAE integration yet?
