I've been reloading since 1975 and I have seated primers deeper when I didn't do the job quite correctly the first time. This is not a regular thing with me but it does happen every now and again. The primer seater is just about the same width as the primer and if you just give enough pressure to seat it (and if you hand prime your primers you can feel when they bottom out correctly.)
I have never had a primer go off doing this. Primers really need a pretty sharp blow to the primer to set them off and a slow steady pressure probably will not do it.
A good explanation about the seating of primers can be found on page 57 of the Lyman 49th Edition (that's newest one I currently have). It explains what might help you make a decision.
NOW, all that said, It is your call to do what you want.
AS A CAUTION, I HAVE HEARD OF MORE PEOPLE SETTING OFF PRIMERS THAT WERE SEATED HIGH WHEN THEY DECIDED TO DEPRIME TO START OVER. The decapping pin is much smaller and as such actually touches the anvil of the primer and forces it into the primer cup and the primer mixture when you decap, thusly more likely to set the primer off if you do it too quickly. If you do this, go SLOW and STEADY - no jerking down on the handle.
Whatever you do, be safe, wear safety glasses and hearing protection (and maybe even gloves).