Just to make our PM conversation public, as this might help others:
Originally Posted by: SkyMix_RMT 
Awesome tool. Is there anyway you could remove the 3000 object limit warning? Or at least increase the object limit?
Hello there,
I have actually taken a look into this just now.
I can remove the message but the popup will still show.. but without the text.
I can't remove the popup as it is not a strict worldbuilder-internal menu but instead it is an official windows warning popup message triggered by the worldbuilder and executed by windows.
I can't edit the part of the worldbuilder that is scripted to trigger this popup message as this part is compiled into an .exe and almost impossible to edit.
Give me the source code of the worldbuilder and I can fix it for you ;)
However, there are 2 possible workarounds for your issue.
Workaround 1:
You could duplicate your map. Use one version only for trees and stuff and the other version for everything else. When you are done with your map open the tree version in worldbuilder, select all trees, copy them to clipboard, open the other version and paste the trees. You could also use multiple tree versions if you have more than 3000 trees.
Workaround 2:
Use your keyboard macro software or any free macro software to create a macro that constantly spams the Return key. Enable this macro when you are placing objects. This will confirm the warning message before it even pops up. Disable the macro when you are done placing objects.