Gate customization is broken. It's excessively difficult to coordinate enough of the right colors to even start experimenting in an intelligent way. Anything you do is quickly buried by other players who add all their crystals. It's only going to get worse with a bigger player base.
To fix the problem, allow players (or guilds) to start their own gates. Starting a gate would cost Energy and Crowns, but if it was popular give you a good chance at making money on the deal.
Once it's created, let the person who starts a gate you set the rules for allowed minerals. For instance, you could restrict your gate to only accept Yellow and Red ore. One way this could be done is with ratio caps:
Green: 0
Yellow: 2
Red: 1
Blue: 0
Purple: 0
In this example, you could deposit as much Yellow as you wanted, no Green, Blue or Purple, and Red up to half of the volume of the Yellow. Allow the gate owner to modify the rules over time to tweak the gate as it's being built.
This way people could more easily customize and experiment with gate creation. Additionally, the playerbase will more easily customize the game to create the levels they want to play most.
I like your suggestion, it's interesting. In the meanwhile you could experiment by adding a dusk drop whenever you're depositing minerals? That way you know the bottom levels largely came from your own deposits and as such are a result of your experimentation.