I think "without being obtrusive" is a key point here, because any type of popups in the midst of working would break flow as well. Fixing compiler warnings is flow-inducing because it's very linear and has a fast feedback loop, so it would have to be something akin to that.

Side-note, I wonder if audio cues would work well here. When another person is commenting on something, we as humans can typically remember their point while still being focused on text, but if a popup with text comes up we usually get distracted by it. Just my two cents.