The problem stems from the roster composition - and the example you gave doesn’t really deal with the severity of the disparity at the top end of the guild GP ladder.
You seem to be basing your understanding of the TW Matchmaking issue on much smaller guilds who already have inactive players, hence don’t sign up with 50/50 because they can’t. But up in the 550M+ range pretty much no guilds have inactive players. They’re signing up with fewer than 50 every TW even though the players who don’t sign up are active players.
If 40 members of a 700m GP guild are matched with 50 members of a 560m guild (so sign up GP is more or less the same), the TW will be a total landslide in the larger guild’s favour because there’s a huge difference between a 14M GP roster and a 11M GP roster.
A 14M roster will have all the GLs, all 3 of the GL Capital Ships and likely all the other important Journey / Conquest units. A 11m roster will have at least 2 GLs missing (probably more) and at least 1 of the GL Capital Ships missing (probably more). Yes the smaller guild has 50 players, but they won’t have the teams in their arsenal to compete with the larger guild.
I think the biggest issue with TW Matchmaking is actually the consideration of recent results, which occasionally gives a guild who have lost a few in a row an easier matchup. I’ve seen my TW casual guild (690M) have 48 sign up but get matched with a 42 sign up 530M guild. We don’t care about TW, but it was impossible for us to lose that.