I had the same hesitation with my story. My story will ultimately have my main character end up with another man, but like yours, romance is a subplot and if i could, romance would be a 4th label. My story will involve some other LGBT+ characters but the reason why i chose to go with BL or LGBTQ+ was because the romance between the two characters is a huge part of the flow of the story and one of the takeaways. VVBG did a twitch stream for Fujocon and Michi made a good distinction between the two. BL does come with the tropes (good and bad) and is more so focused on the relationship between two male main characters (whether quintessential romance or not) and LGBTQ+ doesn't necessarily have to have romance. It better serves as a scope for representation of people within that community. So BL falls under the umbrella of LGBTQ+ but it still has its own little niche. (just the gist of it, she said it way better than that lol(
That being said, i think that with what you described about your story, it may be better to go with the LGBTQ+ label. When you add tags to your story, you can always add "boys love", "BL", "MxM", etc. I stuck with BL and put LGBTQ+ in the tags. And because your story already has them as an established couple, you can have more leeway so to speak that you might not get if it was just BL.