Ahh, I'll fill in what base gates actually are to better arm you (and anyone else reading it) with that info.
So in response to specifically this:
Inb4 getting flamed for this response, but I believe it's coded as minions that are ghosted to just their own team. I'm not an engineer or tech designer, however, so I couldn't tell you exactly why they sometimes feel clunky.
Base gates are a combination of two things:
(1) Selective pathing terrain, each connected to the quality of "team". We added a new terrain pathing type back in preseason just for them. This functions exactly as you would expect them to.
Fun fact: Currently, teams are used as the only quality. They could be specified down due any number of 'dependable' rules. Such as "Ranged champion only" or "Cats only" (though that last one would take a bit more work to hook up).
(2) A new type of vision rule (but only on the inner cells of a base gate). There are four basic vision rules before base gates for terrain:
"I can see into and through this" (most walkable terrain)
"I cannot see into this or through this" (walls)
"I cannot see into this or through this unless I have vision inside it" (Brush)
"I can always see this" (Crystal Scar outer circle)
Base gates introduced a new vision rule.
"I can always see into this and out of this, but not through this."
Now for why the base gates sometimes feels clunky:
Initially to get the vision behavior the center of the gates were actually brush with an invisible minion inside that selectively gave vision of the brush to nearby enemies. When we did this we already knew it was just a temporary behavior, it was just something to hold over until the vision tech got into place. Patch 5.3 removed the minion and introduced the real vision tech for the gates.
However, when we removed that minion... the clunkiness reports were still there. And it seems that they still are (but ideally to a much lesser degree).
The reason for that is actually due to height differences in that area. Basically, the pathing system DOES navigate "vertically" and not just in a 2D game. Height does matter for pathing. For the most part, this isn't significant. Most of the changes in height are subtle and slow.
For base gates however, there was a distinct "drop" that the pathing system actively avoided because it evaluated that as a sudden massive increase in time to traverse. Unfortunately, the inside of the base and the outside are at a very distinct height difference, so even our smoothings that should've cleared most of it up won't clear up all of the behavior.