Her official artwork has her looking very similar to Setzer, sans the scars, and her sprite outfit is very similar to Bartz' except without pants. It's part of her story that she was pretty much raised as a boy by the pirates and she disguises herself as one to keep their respect (except she's so beautiful that some still end up falling for her even while they think she's a man). Her job outfits before the "reveal" are even pretty gender neutral or similar to Bartz', with Mystic Knight being the first to display some cleavage. So if we get Faris' most iconic outfit, it'd be her Amano artwork one, i.e. the Setzer-like longcoat sans-sleeves and the one she's disguising herself as a man with (I'm also a believer that clothes are just clothes, which is my biggest gripe with the gender locked outfits here).
Answering your question, Cloud has become a memetic cross-dresser since he's been allowed to use female-only equipment in his spin-off appearances (Dissidia and Duodecim, FFT); He's not a transvestite in his home game because he doesn't CHOOSE or LIKE wearing women's clothes outside of that sequence. However, Faris CHOOSES to continue dressing "like a man" the rest of the plot (and is visibly uncomfortable in the sequence in Castle Tycoon when she's FORCED to dress like a princess, plot-wise, the characters clothes don't change when they change jobs, only gameplay-wise), while Cloud only CHOSE to wear the dress (and was mostly forced by Aerith) to save Tifa.
Also on the artwork thing
here is her official Amano artwork, very similar to Setzer's coat (and even long hair like Setzer except tied up), except sleeveless with a blue undercoat and white pants, compare
Setzer's.
This other outfit may be more "feminine" but it's still a breastplate/pants/boots combo, just red and with added cape.
This Amano sketch is, well, sketchy but is still a Pirate outfit and cape.
This is the same breastplate, sash, pants, boots, cape combo just more decorated as is Amano's style. Compare her decidedly more feminine sister
Lenna