Well yes and no. Correct you have to collect your bags and recheck. But are they tagged thru and do you have the boarding passes for your connection. In SJU right outside of customs is a drop of to check your bags thru. I do not know if you can get them tagged to anohter airline there. Have never had to think about it.

If you have to got completely out and go to a checkin counter, then leave a lot more time.