They will likely have some Apple specific features, but I doubt they'd want to make them incompatible to the point of requiring a software rewrite compared to other ARM chips. Just recompile your stuff, jump through whatever hoops you need to publish it, and that should be it.
Going by their iPhone chips: nothing special to worry about, other than page sizes which may not be an issue in the future depending on how Rosetta 2 works on their actual shipping hardware. There are some proprietary MSRs but they’re not for your use ;)
