The respec command and a few other things I'd forgotten are on
this page (the respec is the "nanofield reboot").
There are skillpoints you can find in each stage; each one amounts to an instant levelup. Naturally they require going out of your way. The only potential exception to this I can think of is in the last (or is it second-to-last? It's been years since I last played) stage, where you have the choice of either fighting a boss (Asha) or getting the skillpoint, by using a max-level weapon. Getting the levels required to unlock the weapon may be difficult in a speedrun, though.
If you go the entire game without killing anything directly (note this requires getting that aforementioned skillpoint, since Asha, unlike other bosses in a pacifism run, is not killed for you by NPCs; also note that using the projectile reflector to kill enemies doesn't count as a kill), then you'll get the Massacre weapon right before the final boss, which will speed up that fight significantly. On the other hand, this requires you to maintain a truce in sector 2, and the game penalizes your in-game time if you do this for the entire sector. The speedrun by Ultimortal intentionally breaks the truce right before the boss of sector 2 so that this doesn't happen to him.