The only danger of seating the primer deeper is if a granule of powder has fallen through the flash hole and somehow exerts enough pressure on the primer to set it off. Highly unlikely, but if you drape a heavy cloth over the whole press while seating and wear eye protection, you will be OK.
Take the cartridge, hold it in your hand, primer side up and shake gently until you figure any powder sandwiched between the primer and the primer pocket has fallen back through the flash hole into the main body of the cartridge. Then put your shell holder with cartridge back into your press and seat the primer.
As was said before, it is a sudden impact that is supposed to set off primers. Slow pressure rarely does.
But do take precautions. Even though the damage that can be done by a cartridge igniting while it is not in a chamber or other confined space is minimal, bad luck can throw a shred of brass into tender places. Besides, the embarrassment is well worth any precautions you can take. ("But honey, I shielded the press before I started!") If you are married, and your spouse is at home when you do this, it would be best to tell her not to worry if she hears a bang. I have set off a primer before (on purpose, I chambered a primered empty cartridge and fired it just to see how much power and noise a primer had.). If you have a small apartment, your neighbors MIGHT be able to hear it. If you have a large house, someone on another floor MIGHT miss it. It is a worthwhile experiment. Put a piece of paper in front of the muzzle. The burn marks are educational, too.