I agree, chuck everything in at once, let PI sort it out
you can do integrate separate masters and may need to due to processing resources limits. regardless I find an integrated mini-master makes for a better target frame for more accurate registration and a better end result down the line. For example I work dslr so have noisey subs, if i grab a dozen subs and manually register (dynamic alignment) them then integrate them to a 64bit file, this file works much better for automated star alignment of the entire set as well as dynamic alignment of the entire set. there much less problems of noise and hot pixels getting registered as stars.
doing this you could also crop this mini-master to close to what you want and registration then results in smaller precropped files, saving drive space and processing time.
for seasonal imagers you may have no choice but you use multiple integrated masters to build a deep signal for a faint region especially when gear may have changed and automatic processing of various file formats and sizes can comlicate matters.