> I really dislike automatization there because it tends to open your gates when you are fighting with an enemy in front of it

Hence you should use manually-controlled drawbridges for that. This way, we might also get away without having to ask "which door do you mean?"

> You would also be able to control "automatic" defense structures yourself

Hm, doesn't that kind of kill the point of them being automatic? They don't strike me as essential to the design though, so I would like to keep details open.

> What happens to powerlines

We would have none. Currently I'm toying with the thought of having the base aggregate the energy for you - with the upside of no "Kabelsalat" and a nice central location to show your energy statistics. Overlapping base areas could transfer power.

> pneumatic tubes

What should these do?

> when they are connecting two buildings that do not belong to the same owner (one was conquered)?

Hence replacing everything with implicit (magical!) connections using the flag.

> What happens if the enemy (player A) conquers a flag that covers buildings that are still covered by another player (player B)?

Okay, here are a few more details:
* To build a flag, its construction must be initiated and it must be grabbed by a Clonk until construction finishes.
* If no Clonk grabs it at a point during construction or its position becomes covered by an enemy base, it automatically start deconstructing.
* When an (enemy) Clonk grabs the flag after full construction, it deconstructs. If he stops or gets interrupted, the flags starts reconstructing.

Therefore, conquering is actuall a two-step process: First remove the enemy flag, then install your own. The second step might actually be impossible if another flag is nearby.

> After having blast through the concrete

Yeah, that's a problem. Somehow physical access to the flag must be important for the defending player as well. Hm, healing? ;)