Yes, that would work fine. You just have to track when that happens so that you know those two rooms are already merged.
Another option is to generate non-overlapping bounding boxes for rooms, but then don't fill in that entire box. Instead, you can draw whatever shape you want in there.
The maze generator will then fill in the cracks you leave.
Another option is to generate non-overlapping bounding boxes for rooms, but then don't fill in that entire box. Instead, you can draw whatever shape you want in there.
The maze generator will then fill in the cracks you leave.