Most changes will be made by the community via mods. Just look at what improvements the Skyrim, Freelancer, and Oolite modders have made to their games. I feel it would be wasted resource not to involve the passionate Elite community in customised code modifications. After all, its the community who KS funded ED, and FD have already allowed the community to contribute further at the design level.
If they don't have the resources to make any changes themselves, then at least they can allow enough scope for modders to do it. They have already indicated they will provide dev kits for such mods after the initial release. Without the requirement for MP consistency holding them back, my guess is that most of these mods will be for SP.
I do find it interesting that given the choice, most single players at this stage seem happy with what has been offered. That is, they prefer not to use the improved changes listed in the OP. From my understanding the only reason these features are not already in place (except perhaps the true persistent universe) is due to MP/networking reasons ... reasons irrelevant to the single player, but applied nonetheless. I can't help but wonder what this game could have been if it were not held back by it's MP needs. At the same time, I understand MP is important to many gamers, and more importantly, it's developer.
I am not suggesting any changes be made to the MP game, just that it's SP version be released from its shared cage and allowed to roar.