Honestly, the auto-refilling isn't the main issue. It's okay. Or they could adjust ingredients and get rid of it. That'd be fine by me.
The issue comes in when you want to play an alchemy build, or a build that relies on even a little alchemy. Before the Better Combat mod (among many, many other things, it increases potion durations/slightly changes effects), I spent OVER half of each fight in my inventory screen, changing potions around. If you're going to make a system that has you "release" potion effects during combat (call it what you want, it's drinking the potions during combat) instead of preparing for combat beforehand by drinking them, you at least need more quickslots for them.
And here's why this would have been an even better game for TW2's system than TW2: In this game, we investigate attacks before finding monsters when we take contracts. We use Witcher senses - we see footprints - we think to ourselves - we then check the Bestiary and remember that particular monster's weakness. We can then prepare for the upcoming fight properly by using the right potions/oils and equipping the right bombs. Of course, we can only do that through mods now. Because if we use potions before battle they'll probably be done by the time we get to the monster.
Also - even when we're out in the world, we can use those Witcher senses. I use mine all the time to listen to what's around me. Check for those little outward flowing circle things that mean something's there. You can usually tell a monster is near, or whatever, by listening. Even tell what type it is if you think about it a little bit. Allowing us to even prepare for the random! How could we not have pre-fight preparation when we have all this at our disposal?
So yeah. I use mods to do it. And will continue to. I don't see CDPR changing the way it works. And mods allow us to alter stuff to our liking without bothering them. Which is why Redkit2 will be so great (provided the rumors are true and it's waaay more versatile than Redkit1 was).