They like to pretend their matchmaking is complex. I think it's fairly obvious that it isn't complex at all. It is a simple GP matching scheme. Seems the only level of refinement they have ever added is restricting the matchmaking GP to the top 80 of your roster ... if indeed that was actually implemented. Neither mods, zetas, nor legendary characters seem to be a consideration in the algorithm. Which actually makes sense. Matchmaking like that would be a nightmare to code.
At any rate, no sense worrying about it too much. You can either g13 your most effective squads A$AP or just keep developing at your own pace.