Modifying loot drop % and loot tables would make it not vanilla.
It's kind of always been a thing where people run a "Vanilla+" server. Vanilla+ servers aren't Vanilla at all (gather manager, 2-3x loot drop, auto sorter, nteleportation, half-craft, etc, a real vanilla experience...smh), people just lie and it's like SEO. They are popular servers, though! I dunno if it's people like being lied to or people would rather lie to themselves and say they play on a Vanilla. There are also community servers that are modded and shouldn't be in there.
Point is, you can do it however you want. It might not show in the official section anymore, and you might have your server banned. You can get a new IP pretty quick, though. There are tons of shady pieces of shit that have modded servers that they call Vanilla. It's your call if you wanna be like that..