While it's true that Silphymon was created back when Digimon were meant to be sexless, Silphymon is masculine first because of the slight muscled build of its upper body. Gatomon is gendered to be female and Aquilamon is traditionally gendered to be male, but their sex was meant to be undefined. Possibly by the standards of the monster designers, Silphymon ended up predominantly masculine. My reasoning lies in former misuse of sylphs that break the guidelines and defining traits of said mythological creatures. Using Pokemon to discuss gender norms isn't quite enough in the case of Sylveon. Granted, I'm playing the Kevin Bacon game with monster trainer etymology.
Silphymon is androgyne and is only part-male because it is a DNA digivolution of Aquilamon and Gatomon/Tailmon. Of course, this is not to say that Sylveon is exclusively female, or male, or that it can be of both genders, but I think that the comparation is not that good. Although you are right: Digimon can already break the stereotype, why not Pokémon would do the same thing? (despite the fact we already have things like male Gardevoir, or female Machamp)