The intersection of sexuality and gender is a weird one. In a perfectly ordered world, sexuality and gender would be at right angles to each other. It should be easy to express one's gender identity without implying anything about one's sexuality, and vice versa. The world of human psychology, however, is squishier than that.
...which has its pros and cons, I suppose. I mean, if someone happens to take sexual pleasure in some socially-transgressive cross dressing, far be it from me to tell them that their fetish is wrong, y'know? On the other hand, though, I happen to know some people who do get inappropriately fetishized because of their nonstandard gender presentation. It... is not ideal.
Bottom line, I do think, as with many things, the primary issue is whether one is fetishizing the thing or the person. Fetishizing the esthetic of "cute boys in skirts" is an entirely different situation from fetishizing the person who happens to match that esthetic. I think Ellen's in the clear, here, because she's obviously thinking of yaoi twinks as conveniently fictional sexual objects, whereas Jamie is a person she knows and likes and respects first and foremost, with her sexual attraction to him deriving from of that personhood and his personality, not in spite of it.
Like a lot of ideas, I do think dissecting one's own sexual preferences and fetishes is something that can be best done via open conversation. Just having a sounding board helps. I don't think Ellen really understood her own feelings on boys in skirts until Max made her express it just now in words. Much like the Sapir-Whorf hypothesis says your language determines the thoughts you can have, I think that certain things you think you know, you don't actually know until you can actually express them verbally.
Which is to say - I wholeheartedly encourage people to talk about these things. It's the reason why I do things like Sexy Self Comics Day (which is March first!) - I do think that writing about what you like and what you want and what you think not only can be helpful for your audience, but can help the writer as well.