I'm sure there's lots of x86_64 specific code in the macOS userland that is much more than just a recompile - things like safari/javascriptcore JIT, various quartz composer core animation graphics stack and video encoder decoder stack libraries, as well as various objective-c low level pointer tagging and message passing ABI shenanigans and so on. This is probably why 32bit intel mac app support was dropped pretty hard pretty fast, as the entire runtime and userland probably required a lot of upkeep. As just one example, 32bit intel objective-c had "fragile instance variables" which was a can of worms.
This is <1% of the total code that Apple writes
Yeah, the most important, least readable, and oldest code. It's exactly the stuff that's expensive to maintain.
It's not that expensive.