I adore her fics, and especially these. There's a third part, too: The Wild Beast
I like Brian as a daddy a lot, though Gus doesn't have to live with him (them) for me to enjoy that aspect of his character.
I've always assumed that the people who write the Daddy!Brian fics where Gus comes to live with them write them for the same reason that I like them: to see Brian's sentimental side come out. He's allowed to be a little sappy with Gus. Or, rather, he allows himself that bit of outward emotional reaction.
To have a daddy!Brian fic you have to have them adopt, have Justin father a child with a surrogate, or get Gus to them somehow. And while BBC shows it can be well done, I think a lot of writers just aren't that skilled in story or execution.
What I don't perceive, though, is anything directly malicious towards Mel & Linds even when they're treated maliciously in a fic. By that I mean that I think people think Mel & Linds are good canon parents and that children who're raised by two moms (or only one) turn out just fine. I don't think they intend it as anti-lesbian. In the wider sense, I mean.
I think dead!unfit!M/L are just a device for the author to indulge her daddy!Brian kink and most authors do it poorly and unimaginatively. I mean, until Gus is a teenager and able to decide he'd rather live with Brian, if he ever did (and legally, he probably couldn't since Brian's not a custodial parent, but M/L could allow it if everyone was in agreement), but there's no other way for these authors to get child!Gus to B/J except killing off Mel & Linds or making them unfit.