I see where Dizzard is coming from with that. I had a similar experience with the original Warhammer 40000: Dawn of War. In one of the expansions, they put in a map-based conquest game mode, where the bases you would construct within the missions would largely carry over if you were ever to do another mission on that map.
Sounds good, right?
Well, later on they made another expansion, and removed the persisting bases from the conquest mode. That just didn't "sit right" with me. It's something you made, shouldn't it still be there the next time youre in the area?
Granted, in an RTS, that sort of thing has gameplay-related consequences, whereas the example Dizzard mentions really does not. I'm not necessarily saying I think anything needs to be done here, but I definitely can relate to the feeling of something not sitting right, and it interfering with your ability to enjoy the game to varying degrees.