Sure, if you crop a mask w.r.t. to its corresponding bbox, you will have the mask.
During the training, the RPN proposes RoIs that are not necessarily aligned with the bbox (RoIs have a fixed squared size and we’re trying to get match them with regression*), but we have to crop the mask of the instance we are learning anyway: hence the full size HxW masks for each instance.
* Find more info about the bbox regression in the Fast-RCNN paper 2, Section 2.3 and Figure 1.