Arioch, you are a legend!
Krikkitone, your #1 doesn't work.
Even if it was 100 turns to build a new palace, the agressor could never conquer 10 or so other capitals before the first victim has a palace again.
And the longer the victim has to live without capital, the more useless the attempt to build it would be: he would never recover from 100 turns without trade routes and other disadvantages.
So the only logical explanation seems that conquest is all about the original capitals, but you can have a replacement capital for most other functions.
It may be confusing, but I can't find a better solution.