Modding my way through...

[Fingers]

You can add a "structural" flag to ship systems to prevent them from being uninstalled. The main weapons of the starship D....... (which you may have found) work this way.

The ship movements are pretty basic, and can't be modified besides changing the turn rate and speed. This might be expanded in the future to add some interaction between ship motion and weapons (such as weapons that throw a ship into a spin, maybe a recoil like you said). The 1.1 patch concentrates on bug fixes but we may well add new features and content in later updates.

The areas of the game with the most freedom in terms of modding are quests and weapons. Both of these systems are also pretty complicated and I haven't had the time to document them very well.