It's a complicated issue and I also had difficulties understanding the boundaries of that definition. I still don't fully understand.
What I'm going for now, is not looking at the content in itself, but at the pertinence of the content for someone from the LGBT community.
I'm part of it too, and I grew up before the Internet, when LGBT content was hard to find and generally very specific. At the beginning, I was mostly interested by stories about LGBT problems or LGBT romance. But very quickly, and especially when I started having access to the Internet , I became very in demand of any kind of story with LGBT protagonists doing whatever, simply because it was easier for me to identify to them, and maybe also because it was making me happy to see they existed and were shown as average people.
In the case of your story, something that I would immediately think of is this question: do you think your main protagonists would be gay if you were not a member of the LGBT community? If not, if the reason they are gay is because you felt inclined to write characters who have that aspect in common with you, then you can easily understand that it may be the same for the LGBT readers.
They may like to find that common facet with the characters. And if they read your story in part because the protagonists are LGBT, then it's somewhat logical they would call it a LGBT novel, BUT I don't really consider it as a genre. Not even a sub-genre. I really see it as an adjective that precises another genre (LGBT romance, drama with LGBT elements etc...). I myself write a coming-of-age fantasy comic with LGBT elements. I would not qualify it of LGBT comic, especially not for the first chapters that do not even imply any LGBT topics; but at latter time, I would understand if some people do, and I may (depending on how my comic develops, I'm not entirely sure what amount of time I will give to every character). There are several gay characters, I have a couple chapters mostly centered around a transgender character, and in those, I will actually have LGBT related topics such as discovery of identity, rejection from society etc; but it remains a very, very little part of the whole story. Even so, I really wanted to give some space to these subjects, because of my personal experience not only as a LGBT author, but, maybe mostly, as a reader who have been desperately looking for years for content with LGBT characters that would not be full romance or slice of life.
This is merely my experience, but I hope it can be a start of an explanation