Pretty simple one this:
If autosell checked all available eleavtors and sold for the best price, then three nice things would happen:
First: Players would get more coin.
Second: Boosting would work.
Third: People would no longer be able to blame autoselling for creating 'bad' elevators, and would be able to boost as they pleased to influence gate creation however they like.
Oh, and it would enable autosell on a 'not launched yet but materials are full' gate, which would help make the process less confusing. Which would be nice too.
This might work even better if the gate creation terminal was more robust. Have one terminal that shows all the incomplete gates, provide information to the players on the status of upcoming stratum, and offer some transparency regarding what stratum could be created if you distributed your crystals in different ways.
You don't need to prevent players from autoselling, you just need to adjust the game design so that the variance in the autosellers is smaller than the number of people trying to manipulate the gates.