I will try to cover all your questions one by one
— the not allowed rectangle:
You can simply hide the default rectangle with the showRectangleWhenBuildingNotAllowed property set to false.
— building on 0-coordinates:
__towerSizeInGridsHalf: colliderSize/(2*gridSize)-1 // the -1 is added to the original calculation
I ran some tests with it and it seems to work flawless.
Since the entities should be created in the level, the entityContainer of the EntityManager must be the level. Also the PhysicsWorld must be inside the level or the colliders will not move accordingly when the level is moved.
— entity origin:
As long as you are not rotating the entity, using the top-left corner is just fine in my opinion.
If you are still facing issues, could you create a small demo project that contains the errors and post the code here or send them to email@example.com? I can then try to debug them further.