In general there is a lot to like here. My takeaway from this, overall, would be to do something like the following:
1. On each planet, have a "utility panel" that describes a few things like how many engineers you want there, and potentially even what you want them to focus on, as well as things like how many remains rebuilders and so on.
2. These things would be automatically created and would not be something you'd have to come back on and see (hey do I have X number of engineers left?)
3. Having them go into the ship bays I'm less crazy about, because then the logic for "do I stay or do I go" gets kinda complicated in the inefficient-on-the-CPU sense. Probably. Maybe.
I see pros and cons, but overall I think it adds more complexity than it solves.
4. Basically I think of this kind of like the screens in SimCity where you can set the tax rate, set the funding rate for different programs, and enact social policies, etc. I don't think there needs to be a different type of command station for planets at all, but rather you configure these things at the planet the way you want (and if your command station dies, next time you come back it's the same again since this data was at the planet).
5. Various tech unlocks could get you new things that are like the social policies in SimCity (recycling as a new program, etc). But those would cost power on a per-planet basis, so you'd need to weigh where your power goes at any given time.
6. Being able to turn up and down the amount of power being used for turrets in general versus for the other things would be pretty cool. Aka, it's like under-funding your fire department. You can build a certain number of turrets, period, on a planet in general. And you can have those fully powered if you want. Or you can turn those to 50% power for a while to then have extra power to ship creation or whatever you want.
7. Hell, having engineers and remains rebuilders actually doesn't fit super well into the current design in general. In the past those were useful on AI planets, but that means they should cost fuel. But that really doesn't fit with the overall goals here, I don't feel like. Having "battlefield engineers" that are used in hostile space and are a fuel-related ship would be pretty cool, but on your own planets why even have those? Why not control everything from this sub-screen and save any worries about things like engineer travel times and whatnot. Cutting down on the amount of waiting time, and just letting you express yourself through the sorts of screens that have been really well-refined over the years (I'm thinking of SimCity 4, not having played the later ones).