The only part which is planned to significantly change at some point is the obelisk at Laurion. That's planned to be made considerably harder/take longer, but have more items/upgrades you can get from other facilities to make the process easier. So that it becomes more of a balanced choice between grinding to get it as soon as you get there, or exploring elsewhere to find all the shortcuts.
Other than that, any changes are likely to be minor. Even Astrape in this version - I called it a rework because it affected balance quite heavily. But realistically very little actual content changed beyond a few small-medium bits. That being said, if inspiration strikes and I think of a really cool way to rewrite a facility, I'll do it if I think the game overall will benefit from the change. But it is unlikely.