Maybe you just haven't come by the normal schematic yet? I'm pretty sure that it doesn't work the way you're describing with the enhanced or the superior versions completely replacing the normal versions of schematics. If it really does then that's a bug.Is anyone having a problem by which they can't create potions as they have picked up the enhanced version, and in order to create the enhanced version you need the original? There is no way of creating the original as the enhanced schematic has displaced it.
Some help would be appreciated,
Thanks
On topic: I'm not too fond of the auto-refilling mechanic as well, as I feel it's way too easy and oversimplifies where it really doesn't need to be simplified or streamlined in the first place. Sure, it saves time but ultimately takes away in other aspects like immersion or challenge.
As already pointed out you can cleverly bypass the new mechanic and play it like TW1 or TW2 by throwing away stuff, so I guess it's not that big of an issue. I'm sure someone is already hard at work on a mod that fully replaces the current alchemy system with something that's more in line with TW1's or TW2's.