Yes because I have generated files too that I can edit further, and need to send log files, screenshots etc to other people.

One option I often recommend is setting up multiple synchronization sessions targeting different parts of a particular codebase with different synchronization configurations (kept mutually exclusive via ignore specifications). Quite often people want unidirectional replicas for a certain folder (e.g. a build directory) with more standard bidirectional synchronization for the rest of the code. It can be a little more complex to orchestrate, but you can use Mutagen's project functionality or a shell script to automate the setup a bit.

Yes I have that too, node modules are one way toward my host machine so my IDE can use them and a few things like that like logs