It is a common theme in computer architecture for someone to say, 'look I have an awesome new architecture all you need is a clever compiler to make it work'. None of them really pan out (other than in specific applications, you could argue GPGPU is as an example, though that appeared more by accident than by design).

Apple would need a very good reason to produce their own ISA. Sure they like to do many things in house but they don't do everything themselves. The resources required to produce and support a whole new ISA are a major investment, they're only going to do it if in the long run is cheaper than paying for an ARM architecture license. I just don't see a solid argument that a custom ISA and shiny new compiler would give them much (if indeed anything).

Whilst they may be shipping LLVM IR for the watch apps rather than ARM code I think this is just so they can target the compile for a specific processor. Each one has its own performance quirks and especially in such a power sensitive environment it would make sense to do specific targetting.