
Maximised score by exploiting the rebel fleet; in sector 3 or 4 I realised the elite fighters replenish when you save and quit and then restart the game. This means you can defeat as many rebels as your ship and patience allow; in three sectors, I only jumped through the exit once my ship was down 5 hulls or less, so there's actually some room for improvement.
I used a drone recovery arm and a defense drone I, which gets rid of most of the missiles, and a cloak, which I only maximised in sector 7. While it is rare, sometimes missiles get through your defense even with good timing (especially with elite fighters equipped with 3 missile launchers), so you cannot infinitely increase your score. But the most limiting factor is actually patience, as I "wasted" some (many) more rounds in the rebel fleet because I accumulated enough ships already (I started counting the defeated ships after a while and my goal was to reach 300 defeated ships; in the end, I got a lot more due to the precounting ships).
I only destroyed a handful of auto scouts and the boss during the whole game; I boarded immediately into the weapon room of rebel ships with three Crystals and one Mantis. If the locking of the room was mistimed and a rebel escaped to the medbay, I had to evade more shots and rockets, which also adds to the rare hull damage.
Excessively flying into the rebel fleet takes the randomness out of the game a bit; I had no particularly good run regarding visited beacons or weapons (got no really useful weapons other than pike beams, which are good against Zoltan and Boss B).
All in all, I think with exceptional patience and good skills one can go up to 30,000 points or so.
This run was done without mods or cheats or spoiling myself with other people's strategies on Normal with the Crystal ship type B (my first run with the Carnelian!).