Some game formulas, such as the mana return formula, give bonuses to the tune of counting your highest trained mana control fully, and next highest trained one at half. This balances out TP costs and rewards between hybrid pures and pure pures. It is a fair and equitable way to do things.
Other game formulas, such as a few in alchemy, simply average the mana controls for hybrids. This results in hybrids spending twice the TPs for the same bonus as pure pures.
Obviously, all game formulas should use the setup used for mana returns, and the alchemy formulas, and any other formulas in game setup that way, need to be changed. Else this is just-another-hybrid-penalty.