The time span on the tickets must be for getting inside the building. You can stay inside as long as you want except that space for viewing the Pala d'Oro is very limited, so you really need to move through it relatively expeditiously unless you happen to hit that area when no one else is around--which would be unlikely.
I see no references to the crypt on the San Marco website, so I'm guessing it's not regularly accessible to visitors right now. I don't know how reliable the VenetoInside.com website is, or how recently it has been updated, but this is what it says about the crypt:
"The crypt is open to the public on only a few occasions... One of these is our evening guided tour of St. Mark's Basilica: you can access the most important religious building in Venice beyond the usual opening hours to the public and enjoy an intimate and exciting visit that also includes access to this amazing crypt!"
Link to crypt webpage: https://www.venetoinside.com/hidden-treasures/post/the-crypt-of-st-marks-basilica/
So it sounds as if you might be able to sign up for a special-access tour that includes the crypt. However, at the moment I don't see any way to buy such tickets on the VenetoInside website.