I agree with what Cads said, that Any% should always be the fastest completion without cheating. Skipping the final boss, as anticlimactic as it may be, is definitely the fastest method and is not cheating. I do understand that combat skill is an important part of the run and the viewing experience (check out this clip from my last stream :) ), so No-Cyborg being a separate category seems fair. However, this community is so small I worry that splitting the leaderboards wouldn't be a good idea. The visible variable option seems appealing, though.

On the topic of using the cyborg in normal fights too, I admit that I never really considered it in my runs until now. happycamper did the testing for the Mycon fight and seemed to conclude human piloting was necessary, but just now I did a little bit of testing on the other required fights of the run with 'cyborg++' on the ships I normally use for each fight. Here's my results:

3x Chmmr vs 5x Druuge: The Chmmr seem to be unable to win, or at least very rarely. Typically they go 1 for 1-- in one run, the first Druuge actually took out 2 Chmmrs and then 2/3rds of the 3rd's HP. Human piloting is likely 100% required for this fight.

3x Chmmr vs 10x Umgah: The AI beats the Umgah here consistently. However, if a Chmmr was lost to the Druuge fight, the AI will rarely make it through all 10 Umgah with only 2 Chmmrs, only managing to take out 7-8. Cyborg seems to be pretty useful here.

4x Utwig vx 3x Ur-Quan and 3x Kohr-Ah: The AI usually wins here, but sometimes even 4 Utwig is not enough. Considering the fact that this is the final fight in the run if you're using cyborg, I'm not sure if it's worth the risk. I also tested this fight with Chmmrs instead of Utwigs, and the Chmmrs went around 1 for 1.

Bonus: 1x Earthling vs 1x Weakened Ilwrath (tutorial): The AI usually wins here, but not always. Even so, sometimes it takes longer than just pressing manually fire twice and killing the thing. Cyborg is usable here, but doesn't really feel worth it especially when you have to turn it back off for the Mycon fight.

Ultimately, the cyborg trades player agency for speed. You may need 2-3x the amount of ships to win a fight or you risk the run just dying with no ability to play better and avoid death, so is the time spent getting the RUs (pre-endgame) and building/crewing the ship worth the time saved? I think more testing needs to be done. At some point I want to test the AI with Orz ships too, because I think we all know how strong the AI is with ranged projectile ships (Druuge, Ur-Quan, etc). If using cyborg in normal fights ends up being too much of a time-saver (currently unclear if it will) it may be necessary to split the leaderboard, idk.