Being a godparent isnt a legal matter. Its a religious status devoid from any legal institution. All it takes is a parent saying a person is a godparent and a baptism to make it official
Far as I know, the kids know Peter is Spider-Man. I'm pretty sure there were a few issues after the Torch 'died' where he was talking to Franklin unmasked.
As for Doom being the godparent, 1) He's Doctor Frigging Doom and if he wants to be your kids godparent he will be and 2) He's literally been a god more than once and therefore has far more experience in the role than pretty much any other godparent ever.
Also, he saved the life of Valerie and 'requested' to be the godparent. I imagine Reed was feeling generous at that moment and wasn't interested in causing a scene. Besides, Doom takes his roles very seriously and if he's a kids godparent then pity any man, monster or god that tries to hurt them.
Okay, that's just stupid (not you guys, just this concept). How do you go from hating each other to letting said arch-enemy be the potential guardian of your kids? And how does Doom get those duties before and over their uncles, Johnny and Ben??
"Well, Doom may be the most dangerous man on the face of the planet who has tried to kill us all countless times, but god
damn it if I can't see anyone else raising our kids if we both die, Sue."
Let me have a man or woman I hate more than anyone I've ever encountered, a person who has done me serious criminal acts, and see if I even want them eye-balling my kids let alone raising them after my death, over my sister or family taking those duties.
Hitler may be a horrible person, but sure, he seems like the perfect surrogate for children. Lets just ignore everything he's done.
And I'm sure there
has to be some legal channels you have to go through to establish someone as a godparent, otherwise wouldn't family have the right to take in any of the kids? You can't just say "Hey, I'm Joe. Before Sam & Diane died, we talked once and they wanted me to be the godfather. So...I know you're the aunt and uncle of little Becky, but I'm...yeah, taking Becky now..."
Like seriously, I've been all wtf Marvel before, but
W.T.F., Marvel?!