Say that find a used, pre-built AR and a nice one at that. Something along the lines of a LMT, Noveske, etc.

Now, assume you can get the same, used gun in two different configurations: stock, the way it was exactly when it left the factory, or with non-permanent upgrades, such as a PRi latch, stainless accurized BCG, upgraded trigger kit, things that can easily be replaced. Both guns are used, but in amazing condition.

Which one would you rather have? The stock, or the upgraded? I'm asking because I think more people would prefer to get the stock rifle so they can upgrade it the way they see fit, even if the accurized/upgraded rifle would perform better.

I'd opt for the stock one.  Simply in the hopes that it was tinkered with less by the original owner.  A lot of people like to tinker with equipment while not always knowing exactly what they are doing.  Nothing wrong with that, but I'd rather be getting a rifle that did not have any "home gunsmithing" done to it.

I was referring to things such as BCG's and Charging Handles, that can be replaced without any permanent modification. I updated the OP to reflect that.

Tinkering is tinkering.  If they tinkered, you simply don't know what they've done to it because it may not be visible.  Who knows, maybe they clean their chambers with a stainless brush chucked in a drill...  or maybe they ran other "reversible" parts in it that damaged something.

You sure as hell can't trust them to just tell you everything they did, unless it is someone you know.  And even maybe not then.