First of all, welcome back! I've missed seeing your incremental dev updates, and am glad everything's going well now.
I can't say I'm too fond of this change though. At some fundamental level, alchemy used to be a crafting system. 1.1 took away from that somewhat (and made the third ingredient slot almost never used), but it was largely fine because it made recycling items more effective, particularly with the overall changes to how energy worked.
It already seemed a bit odd however to have items that weren't really 'crafted', but it makes sense for wands and missiles, and is at least tolerable for scrolls and potions. My gut reaction for this new proposal is that it just creates too many 1-item recipes, and in doing so alchemy seems much less like a crafting system. The assymmetry of the item types in the interface (some potions would show one option, others two or three, with a haphazard mix or exotics, elixers and spells) also seems quite inelegant.
There is also the fact that a visible catalyst option makes since in-world. What is energy? It's not very clear. However, why does putting a scroll in an alchemy pot create one thing vs another? One particularly noteworthy case is turning normal and exotic levitation into spells. How does that work? Using a scroll byproduct to make those spells seems far more concrete than simply using 'energy'. It is also somewhat irksome to have both a potion and a spell as outcomes for a single input, which are two different item classes.
I also think having at least some sort of item tradeoff is valuable. Scrolls are generally more useful than stones, and three stones vs. a scroll and a stone are not the same from a balance perspective. Sacrificing a scroll for a spell or a potion for an elixir is not prohibitive, but it requires a bit more thought by the player.