I'm not an expert on the ARM64 architecture, or the Switch OS, but from what I can tell, the interface between the OS and the app consists of function calls to the OS api, and syscall-s, that are triggered by the svc instruction. I'd guess the app is statically linked against the OS API, so for the OS calls, the addresses can be patched (or alternatively the emulated OS libs can be mmap-ed to the correct address), and the svc calls can be replaced with a jump to a thunk that emulates it's behavior.

Both seem to be possible, since arm64 uses fixed instruction length. I don't think svc calls can be trapped in-process with user privileges, and it's even less likely it can be done in a portable way.

So probably some level of source-patching needs to take place, but it requires just a high-level understanding of the code, not a full decompilation-recompilation.