Making a custom potion that's just an existing one will likely be slightly inefficient, but not too much since you also have to spend the research on it. I'm still working out all the numbers.
The Omega Potion will be powerful, but it'll be expensive to make as well; it definitely will not be something you throw down in every fight.
I've been floating the idea of dual-elemental potions as an added effect! It'd be some extra work to make it tie in to the status effects, but it'd be pretty cool. An Ice/Wind combo in particular would work together really well, while I can definitely see direct-damage uses for combos like Ice/Fire.
The original plan was to use the built-in data structures to make room for only three, but I've learned more about RPG Maker and JS in general; if I manually make some data structures to hold the custom mixes, I could potentially aim for a bigger number without bloating the gameVariables too much. The tricky part will be getting the crafting menu to play nice with it, but I already have to do that anyway.
I'd really only be capped by how many item slots I prepare for My Mix, as I've got to save some room for other items. The player would have to overwrite a mix after reaching the cap, likely allowing some of the research used for that mix to be put towards the next formula and refunding the ingredients used for any copies of the mix in the inventory. That said, fifty slots should probably be enough.