I think it's because ranking of guilds isn't based on GBG results only -- guilds gain points in other ways. The GBG matchup, on the other hand, is based purely on prior GBG performance, which in theory would seem the most logical way of doing it.
I gather that a lot of the trouble with GBG matchup has been attributed to capping the ranking system at 1000 points: in other words, every time a guild reaches 1000 points, it finds itself matched with guilds that might theoretically have hundreds of thousands of victory points if they had been continuing to get counted. I assume the logic behind this is that Inno didn't want to create an infinite progression of 'leagues' of increasing difficulty (and if they had, that would presumably have brought with it balance issues of its own?) and chose to program a hard limit, with the result that the longer GBG goes on, the more guilds progress to jostle together unequally at the top.
Your assessment seems accurate enough to me, but I think, instead of an infinite progression of higher leagues, the 1k cap could be made to work better if the top leagues penalised poor performance harder. (And I say this while on my top 2 active worlds I am in a guild that stands to lose most from the following suggestion, as I play in guilds that bounce between platinum, <1k diamond, and =1k diamond league.
If there were greater point deductions for the bottom ranks, e.g. in 7th place you'd lose just enough points to end up all the way down in Gold league and 8th place would be well into Gold league range (and maybe only able to promote back to Platinum if you won the Gold league, say? or otherwise spend 2 seasons in gold league in order to promote again), I would think that might 1) encourage guilds to try and achieve 6th place to avoid demoting 2 leagues in one go, 2) add a bit of activity to the gold league, and 3) add a bit more variation to the guilds and activity levels you face across gold, platinum and diamond leagues..
As someone who started a new guild twice in the span of a year, I can tell you the first 2 months of GBG are just plain pointless. There is no activity whatsoever in bronze - gold league and only once platinum is reached do you reach a point where more than 2 guilds do anything at all.