Would disabling the auto save documents option solve this issue?

I think this could work.

.ipynb_checkpoints

"pollution" is indeed a bit of a troublemaker. One area I would investigate is whether Meltano has something of an "ignore paths that match this glob pattern" feature

Yes I investigated the same and came across the use of .dbtignore files. in case someone is facing a similar issue, then please have a look at this documentation https://docs.getdbt.com/reference/dbtignore

Thanks for sharing that!