The problem here is that this essentially turns MC-chan into a side character. She explores, does shit, maybe tosses some people to whatever burgeoning federation or whatever that forms in her wake but ultimately she's a non-participant, she's not a focal point of it and the central conflict proverbially solves itself in the background. I don't like that at all. Rogue trader this is not, and it strips something important, a guiding, concrete objective out of the story. Up to now, that was surviving and rebuilding our ship. Now? Prepare for something bad coming up, but after that, I dunno.
Exploring for the sake of exploring will rapidly become boring, because there is no goal or endpoint to it, and there's always another sector to look into, another people to look into, unto infinity. A quest without a tangible goal, self-assigned or not, will become rudderless, and playing a tertiary role in your own story always sucks.
What I do want is similar, but different. We don't need to micromanage them, but we do need to be a central figure that is the primary thrust of the expansion and combat. We explore/uplift/diplomance/whatever, yes, we get them to join the federation/whatever, but we're also an active participant, taking down threats that they can't, and essentially acting like their deus ex machina (in the traditional sense). We destroy the daemonworld (possibly with backup), they deal with the smaller stuff.
My thought for the quest in general, is that we grow our fleet and we gradually we increase in scope as our forces do like this is a Xianxia, and keep things moving that way without making the spreadsheets too overwhelming, we are an AI after all, and if the Tyranids can make huge ass fleets, we can too with enough research and faith slowly making us into a god. Right now, we see things from the level of an an individual star within the subsector, when we and our alliance take over enough of the subsector and all major threats are subjugated or weaker than us, we'd start seeing the quest from a subsector perspective, repeat with sectors, and so forth. Exploration, diplomacy, and combat would still happens, but at grander scales.