Since Cygames loves to reuse their characters, we got stuff like cerberus_(shingeki_no_bahamut) appearing in Dragalia Lost, same with lily_(granblue_fantasy) who appears in Dragalua Lost too and is actually based on lily_(shingeki_no_bahamut). I've only played Dragalia Lost, so I don't know much about KoG and GBF.

So, what will the course of action be? Alias every character tag with their first appearance tag, or make a different tag for every game?

for characters that have needed it, it seems you take the first game.
I notice most characters that get into granblue from shingeki no bahamut are tagged as such (grea,cerberus,fenrir,medusa).
Maybe Lily was an exception that someone didn't realise was from shingeki no bahamut to start with

Yeah, most of the Shingeki/Rage of Bahamut characters have been tagged as such with only a handful of exceptions: Elta, Erin, Jeanne (except it seems like we're using jeanne d'arc (shingeki no bahamut) for the Jeanne from the RoB anime?), Lecia, Lucius, Magisa, Owen, Teena, Yggdrasil, and Yuel. Arguments can be made for keeping yggdrasil (granblue fantasy) and yuel (granblue fantasy) and I'd personally prefer them to stay as such, but they still technically came from RoB. Can't say with absolute certainty that this is everyone, though.
EDIT: Oh yeah, Lily too, of course lol.

Knights of Glory's problem is that it's hard to tag consistently. This is partially because no one really knows about it, and partially because I have no idea how to handle tagging it. We have cases like Ezelith who's pretty clearly straight from a KoG design (in this case the Elemental Seeker class), so we could just do "create implication ezelith -> elemental seeker (knights of glory)" or something. Simple, right? But then you have people who are based on a design but ended up entirely different, like Rex who is an older and bulkier version of KoG's Axe Fighter, or Ryozen being an old man version of KoG's Buddhist Priest, or Luther and Rawn who just stole the Dancer and Ranger's clothes and called it a day, or Malora and Xander who took some liberties with the Sniper and Runeslayer outfits. We also run into weird cases with the dragons like Midgardsormr who has a parallel in KoG, but it's only called "Green Dragon" and has some clear design differences (like the lack of horns in the KoG art). How would all of this be handled?

Ultimately, I'm in favor of fixing up whatever Shingeki no Bahamut tags need fixing, but handling the Knights of Glory tag is something that'd take a lot of effort and could end up just being confusing and unnecessary.

Magisa at least didn't get named till like Granblue so she's fine with that qualifier.