'The marquis. Well, you know, to be honest, he seems a little bit dodgy to me.'
'Mm,' she agreed. 'He's a little bit dodgy in the same way that rats are a little bit covered in fur."
I'm sure there were elements of the mutant struggle pulled from the Civil Rights movement, but the underlying references to homosexuality were there long before the Legacy Virus.
The simplest of these being the onset in puberty of one's 'mutant powers'. One does not become black after a childhood of being white. The allegory most closely resembles the plight of a gay or lesbian teenager.
"...Doom's enemies have not the mettle to challenge him host to host, tooth to nail... As economic and military options fail them, they resort to simple rudeness."
Basically, you're saying that everything from Lee/Kirby through at least Claremont/Byrne made no sense.