You said earlier that taking out the item from the merchant does the same for the player economy as increasing the price considerably to where no one wants to buy it. I think that's a fine example to what happened to Barkskin, and their intention. Now they made it much easier to make barkskin potions, and increased the price at the vender so now you rely on the player economy near completely.
So why keep the merchant selling barkskin is the question? Well then I say why not keep it? If I can't find a player making those potions, and I can't bother myself to learn herbalism, and I really valued that barkskin potion then I'd rather have it available to me at the merchant NPC than not.
In other words, they're probably trying not to force you to delve into their crafting system if you don't want to, but they're definitely making it more desirable.
Btw, with terrible appraise, I can now buy barkskin at 396gp each. If I was rich I'd see myself buying that If I couldn't be bothered to look to the players around me, but I'm not so I'm going to be looking to an herbalist PC.