Just wondering why this would happen and does this make it neccesary to fire the m1a only when the mag is in?
There is a good reason to fire the M1A only with a magazine in place, but it isn't related to "clearances".
The problem with single-loading this type of rifle is that it has a floating firing pin. The rifle is designed to load cartridges from a magazine, which occurs at a certain speed. If you place a round in the chamber and let the bolt fly, it travels at a higher velocity.
The floating firing pin
may set off the cartridge before the bolt lugs are rotated. This is called an out of battery slamfire and can destroy the rifle (and you). Even in a milder case, where the cartridge fires after the bolt lugs rotate but without pulling the trigger, there are safety issues involved. The problem is, the shooter doesn't get to choose which kind of slamfire occurs...so the safest thing is to assume it will be OOB.
Now, if you loaded the round normally, from the magazine, and
then drop the magazine before firing, that is a different situation. AFAIK, there is no danger in doing this. (No particular reason to do it, either.)