There are multiple ways to define a low% category. Some examples: 1.) no flagship upgrades 2.) no ship/crew recruitment (at the starbase) 3.) minimal artifacts (aka don't pick up the Portal Spawner) 4.) never visit the starbase
Most of these options take a pretty long time to complete (1,3,4) so I'd prefer to realize option 2 for the low% category. The ruling would be that receiving ships as gifts is okay (e.g. 3x Skiffs from Arilou), but recruiting crew or ships at the starbase is prohibited. You can see a concept run I did in the video below.
Concept run:
For reference about the "never visit starbase" (until endgame). I've never done it myself, but apparently someone very motivated did that. You do that because the Melnorme donate fuel to you if you strand in Hyperspace. https://www.reddit.com/r/starcontrol/comments/4byxid/just_beat_the_game_without_ever_visiting_the_star/
No portal spawner isn't that hard to execute, but playing the Hyperspace theme on loop for minutes on end is a bit annoying.
Let's all agree to pretend that the true low % where you wait 2 hours for the Death march so you can skip the Taallo Shield and Ultron parts doesn't exist.
I do kind of wonder about Flagship with Default modules only / no sell - It changes the begining of the run since you can't just buy tons of fuel off the bat, and probbably causes you to visit a rainbow world so you can refuel on melnorme (due to having only 60 fuel max)
Your idea of no starbase recruitment / gift ships mainly changes fighting the Sa-Matra guards (I would probbably drag 1 HP fwiffo through the entire run, killing Ur-Quan with Arilou is something I save for SC1) The change to Druuge/Umgah fights are fairly minor.
I hope people have fun with it but for me just playing an arilou vs Sa-Matra in SuperMelee probbably gets the highlight of this.
Tbh my main concern is finding the balance between enjoyability of doing this category while meeting some condition to be called a low% run. (I mean we could also call it no recruitment, I don't care that much about the name anyways.)
I'd say all these options are doable with some preparation. But I don't believe many people would enjoy doing or viewing runs which are mostly consisting of the flagship slowly making its way through hyperspace. -> I see 1,3,4 being pretty much that until someone convinces me otherwise (with video proof) :D
So for me the only option which I'd consider interesting for both runners & watchers is restricting crew & ships. It is very similar to any%, but you see a different set of ships in battles. Is this interesting enough? I don't know, but I hope to find out in this discussion.