V3 file extension should not be the same as V2
V3 files are not compatible with V2, and therefore should have been assigned a new file extension.
It is expected that finished V2 scores with complex layout are not "reworked" in V3 but kept in V2 and that people keep V2 available on their computer because reading these files with V3 respecting the V2 layout is impossible (or requires possibly long rework of the file).
The choice to not implement V2 layout in V3 to keep the code manageable and maintainable makes sense (even if end users would have preferred otherwise).
But asking to use different folders and to remember which ones contain V2 scores and which ones contain V3 scores is a pity.