Larian Studios Forums Divinity: Original Sin 2 Divinity - Original Sin 2 - Suggestions and Feedback Stacking bug & disappearing container

I wouldn't call it a mess, it's how the engine is built.
And there is nothing to fix, because it's not broken. If you want version 2 out in 2017 then you have to live with it. Although I don't really know how things work internally, I have some idea how much work it would be to do this 'fix'.

I admit that I haven't too much info about version 2 and I don't have the EA, but I believe that they did not change everything between version 1 and 2 (besides graphics). Not the basics, they probably still have this root template - stats - scripts - ... system they had in version 1.
They might have extended the root templates but they already did that between Classic and Enhanced Edition. It did not change the nature of how things work.

(I would personally rather have Larian clean up the Osiris and scripting API and bring way more consistency into them and let modders do a lot more things than we could in version 1. There are at least two mods for EE that deal with inventory mess, so a lot of these 'little things' can be done with mods too.)

And about the 'mark stolen thing'. There have been millions of threads about how bad it is that everything could be stolen and sold without consequences in version 1, so Larian acted. With the current system in place, stolen items simply must be flagged and must become unstackable because the 'is stolen' flag would otherwise get lost when an item is put on a stack.
People wanted it, now they got it.
Identical stolen items on the other hand might build their own stack, but not if the owner is also included and is different for two stolen items.

As said in the previous thread, items (objects) must be absolutely identical to be able to stack. Because they have to be restored to what they were before being put on a stack.

Now, there are some items that could stack but do not because the root template has its 'MaxStackSize' set to 1. This can be changed of course, but not for weapons or armour, because those never stack, no matter what they have as 'MaxStackSize'.