You can push the rhinestones in when the resin is tacky. They will stick, but the resin itself is very flexible. You have to be careful that you don’t distort the shape of the piece. You can see how resin is flexible partway through the curing process here: https://www.resinobsession.com/resin-tutorials/diy-tree-ornaments
As for casting resin stones, then casting a resin piece behind/under them, you will need to find a way to cast the stones in place first. That will require casting the stones in the mold (thus several turns and several castings).