"Trainer-san" is gender neutral. The only argument you have for otaku self insert is the girls using "onii-chan" once in a blue moon.
How is it gender neutral if some call him onii-chan? It's not once in a blue moon, it's how all the younger girls call him.
It's clear you are making an argument based on other games and not this game. Worse, you are then projecting your judgement of the game onto the anime that has male and female trainers.
You can't deny the intention of a work. Im@s has female producer. It doesn't chance the fact that you can only be male in the actual game, so a female producer would never be MC.
But since you tried painting the young horse girl being raised by her second mother as creepy Im not sure what to say at this point.
The whole horse thing is already creepy, but then you have things like the groping (the girls kick him? Right, like horses do. How about making other people actually react to his actions, that are clearly wrong? He did that in public and no one cared). And phrases like "hold tight to her reins". It might no be the intention, but it is creepy.
Thing is, when you keep defending that she has two moms, you're implying the show is relevant to yuri. I'm just saying it's not. I'm pretty sure they'll never imply the two mother's were a couple, to begin with. It's just a gimmicky and a way to not put more male except for the self-insert.