It would probably make sense to separate the hitboxes for structures into a passive blue hitbox and an active orange hitbox, and I do think that it is a good idea, as it would make it more clear to the player how and where structures interact with things. For now tho, when it comes to the gates, if you want to place stuff overlapping their door hitbox, you can open the gate temporarily by inverting it, then place the structure, after which you can close the gate again.