As to mismatches: yes, they are bound to happen in some cases. Even for line-based diffing, Git uses rather convoluted heuristics to avoid them (with the "histogram" diff algorithm), but they can't be completely ruled out there either. I hope that with enough safeguards (helper to review merges, downstream consistency checks with local fall-back to line-based diffing) they can be lived with. I'm happy to try other matching algorithms if they are more promising though (there isn't much coupling with the rest of the pipeline).
Concerning tree-sitter, I have noticed some small issues, but nothing that was a show-stopper so far. I actually like it that it's designed for syntax highlighting, because it's really helpful that the representations it gives stay faithful to the original source, to avoid introducing reformatting noise in the merging process. Parsers written for a specific language can sometimes be too zealous (stripping comments out, doing some normalizations behind your back). That's a problem in Spork (which uses Spoon, a pretty advanced Java parser). And the uniform API tree-sitter offers over all those parsers is just too good to give up, in my opinion.