I do this on Delta all the time. You should not have an issue.

For the people with carry-on, you can in fact go directly to the gate which is in the D concourse. There are no services in that concourse so grab food or drinks before hand. I have checked in as last as 30 minutes before the flight but they were not happy about it. An hour is good timing.

If you do have checked bags, you will need to exit security to pick them up, check in at the IC ticket counter, and clear security again. I use TSA Pre-check and never spend more than 5 minutes in SJU security. The check in process can be very slow at the ticket counter but as long as you're in line pretty 60 minutes before the flight they are pretty forgiving.

FYI - depending on your tastes, there is a great wine bar with good food at the beginning of B concourse or a Margaritaville in the same location. Both pretty good options!