A: Yes and no. An emulator emulating only the Motorola 680x0 CPU wouldn't be completely compatible with a "real" Amiga. To some degree, directly or indirectly, many Amiga programs, beginning from the Amiga operating system, and even some file formats (e.g. because they reference some Display ID, or like IFF-ANIM which makes assumptions about pixel arrangements in double-buffering screen modes), rely on some custom chip functionality. While it would be possible to re-write the software, this is not in the spirit of emulation, and it would be almost impossible to re-write all older software.
Also, it must be considered that when a program does not make specific use of a custom chip's functionality, this does of course not need to be emulated, so there is little or no performance penalty (although there is a certain complexity involved in maintaining the proper timing and synchronization of the various custom chip components, even if they are idle). Setting the Workbench screen or any other frontmost screen to a Picasso96 mode (which, like all RTG modes, does not use the custom chips) instead of an Amiga PAL or NTSC mode (which use the custom chips) greatly improves the emulation speed. Disabling audio in the emulation settings can also slightly improve the speed of emulation.
Specifically emulating certain aspects of the Amiga custom chips also allows the emulation software to recognize certain specialized tasks, and better emulate these by using similar and specific capabilities on the host environment, if possible (e.g. for blitting, which for example is very fast using the Picasso96 extensions for UAE, which are included under license in Amiga Forever).
Please refer to the chapter on Amiga emulators for additional information.