Don't let any sealant get within spitting distance of the drain holes...
(True story...)
Back in 1988: I bought a full-sized Chevy Blazer. It was a great vehicle, but the roof leaked!
After many trips to the dealership for sealing, resealing, and I think an exorcism: it turned out that the drain holes had been filled with silicon sealant by a "joker" at the factory...
This vehicle had been built right before a strike at the plant...
We cleaned those holes out, and everything stayed dry!