Transport ships don't figure into it. (Should they? Seems more like a job for player micromanagement or for higher-level AI, not for the pathfinder.)
Group movement isn't handled specially yet (it'll just do fifty separate pathfindings). There ought to be a group/formation system so it computes a single long-range path and then each unit uses the short-range obstacle-avoiding pathfinder to chase its position in the group, or something like that.
There's no optimisation for unreachable destinations yet. That probably would be good, although if you select an unreachable target then the unit should move to the closest reachable point so I think it'll still need to do some kind of non-trivial search to find the goal tile. Also I expect it's a bit trickier when the goal is a circle/square (e.g. when an archer moves into attack range) rather than a point, because you can't simply check reachability of a single tile and there's too many different ranges to let you precompute it all. The complexity may still be worthwhile for performance, though.
There's loads of algorithmic optimisations that are possible - currently it's just a dumb brute force tiled-based A*, which is adequate for now since computers are good at brute force (it only takes milliseconds) but it really ought to be replaced with something cleverer. (Plus there's a dumb brute force visibility-graph A* for short-range obstacle avoidance, which is probably harder to optimise (everything keeps moving so you can't precompute much) but still has plenty of scope for improvements). My focus was on getting the gameplay functionality and the interfaces with the rest of the system working, so we can get on with testing the game, and hopefully someone with more time and/or pathfinding experience can improve the implementation in the future