I’m starting to wonder if the ‘death’ of the Master at the end of Series 3 was planned. And by that I mean planned by the Master himself. We know his wife is returning, and we know he was on Earth 18 months before the events of the series Drums, and we know the Doctor didn’t met him before that. So what if the Master planned that if things went wrong (because they always do) he had an escape plan. He was killed. And failing anyone else to do it, his wife would step in and take the shot. Perhaps he wasn’t really dead but drugged or something.
It might be that his resurrection is a result of being brought back by the TimeLords during the Time War. There is so much we don’t know about the TimeLord ability to regenerate that it is possible that he is able to delay the regeneration and when it does occur he is better able to control it and keeps the same face but with some physical characteristics different. (blond hair).
Remember, we never see who is actually wrapped in the white cloth on the funeral pyre. We just assume it is the Master.
A stretch I know but it’s the only thing that makes sense to me and accounts for all the odd variables.
I could also be way the frick off base and it’s something totally off the wall. ¬†Remember, in Doctor Who, they have to be able to explain it, but it doesn’t have to actually make sense ;)