It seems to be that gadael can be used in a wide sense of leaving, while ymadael has a narrower meaning, implying some kind of personal departure, physical or metaphorical.
So, you can gadael your wallet at home but not ymadael it there. You can gadael or ymadael your home itself.
In my (limited) experience, in everyday spoken language, not everything is pronounced the way it's written -- e.g. beth might be pronounced be', gwybod as gwbod, fy mod as bo' fi and cyntaf as cynta.
Whether that's a case of "silent letters" or simply diglossia (the spoken language is not identical to the written language) might be a matter of definition.