I never seem to see them outside user shops.

They do, but since Maleria ask for them frequently, they always sell out in less than a minute.

We really need more consumable battle supplies besides the overpriced healing potions, namely dark potions and pylonics.

They're supposed to stock at the Apocalyptic Apothecary but hardly ever do since elixirs were added to the shop. The Burning Chance vending machine gives them out so you can try there.

You can get them from Burning chance, but it's going to take some time to stock up. On average, they only dispense about 1 or 2 of each if you vend your limit. Also, high normal rarity items don't vend from BC, so you won't find any negating pylonics there.

I grabbed some Negatings two days ago.

It is my experience that more of the consumables stock there more often since the elixirs were moved over. It has to do with how the new restocking works.