Without knowing the details of the guilds it’s hard to know whether one prioritises TW omicrons/squads, or if they just have more (and better) DCs which don’t count towards GP. Those changes can massively impact TW performance with similar GPs. Either way, there’s actually a really simple solution to this: more GP bands at the top end with better and more rewards in the top bands.
That way you force the biggest guilds to prioritise engagement in TW, as at the moment lots of players just don’t care for it. It’s not intentional sandbagging (although I know many will contest this fact), it’s just a lack of care because the modes rewards really aren’t that great compared to other modes that need equal time investment. More GP for the top bands would mean more players signing up in the bigger guilds, and so fewer mismatches on average GP per player.