When a ROM is compiled, the compiler follows the build file, which means it’ll build in dependencies related to the files bing compiled. So simply remove/replace has a high risk of not working, since dependencies are unique to each file/component.

There's not really anything special here. This is how any software is built. Components have published APIs with which they interact with other components. The whole point of microG is that it emulates the same api as com.google.android.gms. I'm not expecting a 100% flawless implementation.

This is a bit messy - rooting is done to a running OS, and unrelated to flashing a stock ROM. Stock Roms, as far as I’ve seen typically have Google Services baked in. Just clarifying.

This just isn't true, at least not in my case. I obtained a stock android ROM from samsung's update server using bifrost. I then patched that ROM using Magisk and only then flashed it. So it's patch then flash.

Running without Google Services makes a fast phone and a battery that lasts noticeably longer. You could try simply freezing the Google Services files with something like 3C Toolbox (once rooted, of course). I think 3C can actually uninstall the files, but that’s a good path to boot loop (ask me how I know 😁 ).

Even just freezing the files will often cause repetitive error notifications.

This doesn't really seem sensible? Of course just freezing google services will cause errors. MicroG is designed to emulate google services and mitigate those errors.