>What should these do?

Well, for example transport items between buildings. Or let's say we are going to have (dwarf fortress) mechanisms that link two structures where ownership is important. Something like that.

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

If you would have to stand directly in front of it to heal it would not even achieve what you wanted it to achieve in the beginning :P
Also: I imagine the base to have more than 1 flag. So it can be nothing that access to one flag could solve. ("I cannot heal at my defense flag? Well, whatever, I got 1000 more")

>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.

So you cannot blow it up with explosives?

>We would have none. Currently I'm toying with the thought of having the base aggregate the energy for you

Could work

>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?"

Mhmh, but you DO have the concept of opening/using stuff with mouseclicks, right? So let's say we have automatic doors you could for example still lock the door (dwarf fortress like)?

>They don't strike me as essential to the design though

Essential would be the following questions (that's what I aimed at): Can you control stuff without physical access and only using the mouse? But from what I understood until now that would be the case