Is it possible to import a vector layer into an ROI? Something similar to importing a vector layer into the Processing area in Pix4D Mapper?
At the moment, I use Pix4D Mapper for this type of projects, and with this amount of data (about 8000 photos) Pix4D Matic should be much more efficient.
Such functionality can also be useful when performing cyclical projects (e.g. once a month for the same area). Then you can compile data for exactly the same region of interest