I think you can read whatever you like into characters shape shifting. I think it comes along with things like headcanon. If someone reads a shapeshifter or disguise as transgender, I think that's their right to do so. If they associate with it, that's their right too. It's entire up to a person how they headcanon and how they read a character and how they identify and relate to a character.
Gonna go on a ramble about the differences in cultural differences and readings for a second and that fits into the pre-2010 trans representation OP was talking about sorta, skip to the last paragraph to avoid:
Of course the problem with this in canon rather than just a persons specific personal reading, especially in Japanese media, and older Japanese media, is cultural differences. For instance, to get mildly contraversial and please don't kill me, Grell from Black Butler, as I have mentioned briefly before, is considered canonically trans by the overwhelming majority of western fandom as a supposed character interview confirms. Japanese fans have all but given up pointing out the author consistently refers to Grell as a gay man, that was an unauthorized translation that takes a lot of liberties, and that Grell actually is more in line with a, thankfully not very prevalent anymore, stereotype that essentially conflates being a gay, trans, a drag queen and a pervert into one character who wants to be treated as "the big sister" and uses typically female language. Of course, they're generally met with hostility and death threats from western fandom for pointing this out.
The point is there's a difference between what someone reads and what canon says, neither is entirely right or wrong, but you have to be a bit careful. And obviously it depends on the context. Disguises, don't really fall into the same category, I mean cosplaying the opposite gender doesn't make you trans so why should a disguise. I think it's more about the character and how they feel rather than something as superficial as they changed their form or their look.