Ideas
So technically what I was saying is that's not a mod issue actually 🤗
TOOL makes it easier to place objects outside lots and makes it possible for objects you can't carry, but the issue itself of object disappearing (the one the author is reporting) is related to how the game handles objects outside the lot when loading a residential rental.
When the issue was first observed, I was among the people reporting that to TwistedMexi and they added this fix into their mod, it makes sense as placing objects outside the lot is a key feature of TOOL, so it makes that issue even more impacting for players using it. But the issue itself is from the game and can affect people that haven't used TOOL to have objects outside lots.
For checking if the objects became invisible, it's something that the average player cannot really do (as it requires knowledge on how to use Sims 4 Studio to check objects on a specific zone). But for the issue about those invisible objects, it's not the object itself that became invisible, it's a copy, the real object is deleted when loading a residential rental 😊
You are right. It doesn't make any difference whether e.g. an apple tree is placed in a neighborhood by the game or by T.O.O.L. All stuff will be moved to the zone object data when entering the lot.