A good example of this that I came across when tagging recently was Lily Hoshikawa from Zombieland Saga, which is unfortunately a spoiler for me since I hadn't seen ZLS yet :(
The wiki for ZLS uses female pronouns and mentions she's the first transgender character in a "popular idol franchise" (weird I didn't think ZLS would be described that way...) and that it isn't even HINTED at until episode 17 where even then it's incredibly subtle (color combination of hair + bow, entering men's bathroom)
Apparently that was enough for this to make all the art clearly depicting Lily as MTF though.
I'm fine with it, I'd probably fap to it, but I definitely understand why we should have a good conversation about how to tag it.
Obviously "loli" is going to offend those who don't want to see their lolis with dicks, while "shota" would offend those who accept Lily as a girl.
I despite underscores and like to avoid them wherever possible, so I'd prefer "transloli" to "trans_loli" if we go that route. Much as I've been using "futaloli" rather than "futa_loli"
We could probably benefit from studying how the furry community handles this. In the case of e621 they use the umbrella "crossgender" as oppose to "transgender" and they have a big dropdown display at https://e621.net/wiki_pages/851
Their version of "futa" is "intersex" which falls under four types:
andromorph "An intersex character with a masculine body type, a pussy instead of a penis, and no breasts."
gynomorph "entirely female in appearance but has a penis, balls, or both instead of a pussy"
herm "characters with both a pussy and a penis. "
maleherm "A hermaphrodite who has a masculine appearance, generally emphasized by a lack of breasts."
I don't know if we want to aspire to that level of complexity, though with copying loli/shota stuff over from there we're bound to get the tags anyway.
If we're going to be making unique loli/shota based tags for this booru anyway, we might experiment with further levels of brevity in constructing portmanteaus. For example what if instead of futaloli/futashota we called them foli and fota?
Although now that I think about it, I don't instinctively know the difference...
Some of the special e621 are based on whether or not futas have breast development which obviously is going to be a lot harder to diagnose with loli futas since their mosquito bites get confused with shota chests on occasion.