That first bullet point Collapsed the code for the AI goals AIM_FLY_TO_SHIP and AIM_WAYPOINTS into one sub-function (removing the redundant code).
has got my attention...
Do these changes bring us any close to being able to dynamically issue move orders (working through a ship's normal flight AI instead of manually messing with the ship's controls/velocity)? I ask this because one of the major issues that got in the way of the FS-RTS mod's progress was not having any way to issue move orders. Even though that project's kind of mothballed right now, I'm still curious about how far off that capability is.
I didn't really change anything there other than removing the duplicate code.
Assuming that I understand your question correctly. In short the answer is no, this code does not affect the waypoint management code or the maximum number of waypoint lists (currently 32) or the maximum number of waypoints per list (currently 20). And no, this does not really make it any closer.
That being said, there is no reason that I see that waypoints (and waypoint lists cannot be created/destroyed dynamically if they cannot already be) as the waypoints themselves are just objects of type OBJ_WAYPOINT. There is also no reason that the specific data structures cannot be made dynamic so that the large numbers needed by an RTS would be possible.