I'm glad you're enjoying the mod!
Yes, the condition overrides are still applied even if the related features are disabled. As far as I know, there are no compatibility problems with any other mod related to the condition overrides, and they don't change drop tables. If you're still worried, you can delete or comment out all the conditions in the market conditions csv file to stop the overriding.
I've tried to keep the features page updated - what features did you notice are missing?
The newer structures that require the user to enable them in the settings for example, like the Harmonic Damper or the Planet Cracker - unless a player looked at past changelogs, they may not know about them without having already downloaded the mod and looked at its files.
I have another question and a piece of feedback:
Do stations built in a system already claimed by another non-commissioned faction eventually trigger the launch of saturation bombardment fleets the same way planetary colonies do? Or are they exempt from that rule?
When a station is done building, the standard "You fleet goes into orbit around x" screen pops up. If you have stations set to instantly complete that's fine (you're on top of it), but if you don't (delayed construction option turned on) that screen will appear no matter how far you are from the station when it completes - allowing you to interact with it as if you were there (i.e able to visit the bar).