You have a point, Muffin. (The following was a thinking-out-loud early in the morning kind of deal...)
As an ordained Buddhist, I have mostly experienced support from my fellow Buddhists (of whatever gender) - but the few who are uncomfortable with me transitioning tend to hide their own discomfort behind Buddhist "principles" to do with contentment in general, not sexual issues. That is, they say "you should practise being content with what you are." To which I reply, "I have been, this is why I'm making changes in order to better be 'what I am' instead of continuing to try to 'pass' as male, which is deceitful." This is all just game-playing, of course - I know these people are just masking prejudices. I'm glad there are so few of them, but that's what seems to be going on in Thailand.
Oh, it just occurs to me that what's also an issue for monks/nuns is that they don't just practise the five precepts, they have monastic precepts which include such things as not wearing makeup/perfume - I think the idea is that it's assumed you're dolling yourself up in order to attract others (which makes it harder for them to be content) and to get attention (which is shoring up your ego). It's a weird business - there is clearly a mix of genuine ethical concerns and cultural judgements in the application of these principles as "rules". Something I'm still learning is that the point of having training principles (which is what the Buddhist precepts are), instead of commandments/rules, is that you are forced to be aware enough to have to figure out how they apply in different circumstances, instead of falling back on "it says this and it always means this."
There's more: in a culture such as Thailand where the monks/nuns are supported financially by the lay people, there is always going to be pressure (spoken or unspoken) to conform with what the social norm is, out of fear of losing that support. So I imagine part of the impetus for the Wat trying to de-trans their monks is because the local laity are not comfortable with trans people (if it's not simply a case of prejudice on the part of the monk running the Wat). This is a problem that's endemic to monastic communities that can't support themselves - the need for approval from the laity means it's harder to challenge prejudice and local beliefs.
And finally... in culturally Buddhist countries like Thailand and Sri Lanka, there's a general thing of boys becoming monks for a year or two as part of their upbringing (it's like a gap year before college) - so the boys and young men becoming monks are not necessarily there out of a personal desire for the monastic lifestyle; they may just be there because it's expected of them. I'm not sure why I'm mentioning this, it's just that it's part of the picture.