Apart from possibly not getting any use of a trapdoor memory expansion in a 500 plus, they are identical.
What do you mean? The a500+ has 1mb of chip ram on the motherboard, if you want more ram then you can use the trapdoor.
Incompatibilities are software caused. Software can be patched.
If you find hw that is not compatible then it is to my best knowledge a first, and it would be extremely interesting to hear about.
Hardware needs software too and original floppies can't easily (and shouldn't be) patched. It depends on how original/compatible you want to be, whdload is great but it's not exactly the same.