Ah yes, the question I'm asking myself since years..
Still no definitive answer, but I went for the pros/cons strategy, and see how the proportion of pros vs cons evolves as my story advances. This is for the case of Tapas or any other case where I can change category/tag as I go.
Pro putting my story in the LGBT category
Most of my cast is LGBT
I am a LGBT creator and it apparently shows in my work even when LGBT themes are not involved (for eg. I am NB and also have difficulties perceiving other people's genders, thus my characters are (apparently? I can't see it myself) gendered in an 'unusual' way, which make some people hesitate on their gender; and I also had some NB people guessing I was NB without me telling them, only from my comic).
There are two chapters speaking mainly and directly of LGBT related themes.
I personally love reading about LGBT characters in genres others than romance or entirely LGBT-themed stories. This is something that I missed enormously growing up, and I think it is a shame if it exists but cannot be easily found because it is not tagged so, and thus get lost into all the other material.
It is useful as a warning. I don't give a shit about homophobes, but I care about people whose families, environment etc is a threat. I had to warn a few real life friends about the existence of LGBT themes in my work so they could read it when they are alone and safe. So, I feel the need to do the same with anonymous readers.
Cons about putting my story in the LGBT category
Although my cast is mainly LGBT, it's not really something that is important for most of the story.
Only about 1 chapter out of 5/6 has significant LGBT material. It may be disappointing for someone who would read my story mostly for that.
The first clear allusions to LGBT content come pretty late in the story.
Despite my feelings about the need to warn people as explained earlier, it is still very difficult for me to warn people about what I am. It is very, very uncomfortable, and much more difficult when it comes to strangers (much more difficult than to tell my IRL friend with the homophobic mother that there will be LGBT content and please read it in your room).
So first I only put a LGBT tag, because I thought it was a good way to give people more info if they wanted it. Maybe not for actually searching the tag, but for informing on content the person who would be about to start reading.
When the multiple category came, I put LGBT as a secondary one, same idea, as extra info. But I did not think putting it as main category was fair, because I felt it was going to disappoint people specifically looking for LGBT content.
HOWEVER! When I will be publishing a later chapter, that focuses almost entirely on the teen years and early adulthood of a trans character, I will switch to LGBT as a main category. Because I think this chapter will be exactly what kind of relevant content should be found under a LGBT category, and also that chapter is possible to be read alone, so someone who would only be interested in this section could find it (and hopefully read the rest too, but this is their choice).
So, in conclusion my strategy is balancing pros and cons and not hesitate to change my categories when I feel it makes sense to do so.