Auto-pot function on Mir3 was different for 2 reasons:
1) The pots were instant recovery (Like Sun pots in Mir2).
2) They had a delay between usage.
This made the auto-pot function not only viable but necessary, as there was no "visible" numbering counter on the pots, so it was not obvious as to "when" you can re-pot again in dire circumstances.
You could almost remove the auto-pot function in Mir3 if you at least replaced it with a visible countdown on top of the pot itself. However, Mir3 have those stupid "Pills" that stack as well, act like sunpots, weighed less and they introduced stupidly big versions such as XL, XXL and XXXL lol, so honestly regardless I think personally that Pills broke any competitive edge Mir3 had in potting functionality with these alone.
Mir2 originally had use for Bundles in order to control inventory space, as you've mentioned. However for years now, this was rendered useless, even by the official version. In beta days, you only had S, M and L versions. By the Lv.40s or so, it was easy to massively pack your inventory (And that of Warriors) with a bag full of Large bundles, making you have to be careful between RT bundles and HP/MP etc.
Now? We have XL...and XXL...these weigh a ton and will never cause you to be concerned over bag "space"...this is why Stacking has become a QoL feature, because the only question remaining is that of bag Weight because of the introduction of XL and XXL.
This is usually what I mean by people not taking the extra time to think about functions lol. You could in theory remove XL/XXL bundles/pots and cause the restraint you're looking for...but people have become very use to them :P
In Mir3 official, they actually have the Pills blocked from the auto-pot function, otherwise not only would nobody ever die in fights (This was a common problem in Zircon files), but made Sunpots useless. I don't know if this was addressed in other follow up Zircon servers, or whether Pills remained usable in the auto-pot function.
But functions and additions of things like this, need extra thought because they can change the game in ways you wouldn't think about usually.