RegFan, why did you bump a 5 month old thread? In fact, how did you even find this thread in the first place?
Why wouldn't one bump up an old thread? Is it forbidden? I find it far preferable to starting new threads on similar subject. And why is it a bad thing to resurrect a thread, if it contained interesting discussions that would otherwise be lost?
DS9 was both the best, and the worst at dealing with LGBT issues on Star Trek.
It's actually quite sensitive in the way it slips acceptance under the radar. For example, Dax works out the "male" Pel is in love with Quark, and urges "him" to go for it. This suggests two things: that Dax sees no problem in gay relationships (unsurprising for a Trill), and that she thinks Quark might be open to the possibility. Then there's "Rejoined"; everyone expresses surprise that Jadzia and Lenara can't have a relationship, even the religious Kira. Their gender is never an issue.
"Chimera" is a pretty clear allegory for the struggle for LGBT acceptance, there's even a reference to "Changeling pride", and Odo and Laas are told what they get up to behind closed doors is their business, as long as they don't hold hands in public. Laas is very much the activist, who wants to change form and link with Odo in public, as that's who he is, and he doesn't have to apologise for anything. Odo's more timid and closeted, trying to make himself fit in with the rest of the straights... er, solids. He's even got a beard.
That comparison worked until you took it too far, especially with the "beard" thing...

That's where it kind of broke down.
I agree with all the main points you made in your post - however, the Founders are much more directly relevant to the subject, in-universe, without making them into a metaphor. Well, not really to the subject of homosexuality, but certainly to the subject of transgender and transsexual people.
It always surprises me that so few people ever mention the fact that the Founders are sexless beings who are nevertheless assigned genders on the show. The fact seems to go mostly unnoticed by the fans, and the show itself never did much to point it out. I think more could be made of the constantly ignored fact that Odo was not biologically male any more than the so-called Female Founder was actually female. The show emphasized Dax as a trans-gender/transcending gender character, but when you think about it, the Founders are an even more interesting case, since they are sexless and could be any gender they chose to be - and, with it, any physical sex they chose to be. Theoretically, Odo could change sexes any time he liked and became female or male any time he chose to, but instead he prefers to stick to the male gender/physiology/appearance, just like he always sticks to one and the same physical humanoid shape - that of a middle-aged Bajoran male resembling Dr Mora Pol.
This could be regarded in two completely different ways. One might say that people - fans and writers alike - can't see past appearances, and are quick to assign classic male/female gender roles to everyone: so if a character is played by a male actor, everyone thinks of it as a man, and vice versa. Or, you may say that the fact that none of the characters in the show, including Odo himself, never doubts Odo's maleness, could be seen as a most progressive message about gender that Trek has managed to convey - a Founder does not have a
sex (physiological and biological characteristics of being male or female), but can have a
gender (a socially constructed role), and Odo clearly has the latter, which has become an essential part of his identity. (Unlike the "Female Founder", who, I presume, is only assuming female gender in order to be more appealing to Odo.) In other words - you are not considered any less masculine or feminine, just because your gender is something you have
chosen, rather than being born into?