Interesting. As far as I know, Aurora does not support making a sublight journey between stars, so are you planning on SM-spawning the generation ship in your starting system?
I feel like the generation ship could use more CIWS. It's only got, what, the one turret? In game terms, it might be able to fire in any direction, but in real-life terms that's only going to have a hemispheric field of fire. Plus it's vulnerable to being overwhelmed - and a 5 million ton monster is definitely a case for "overkill it NOW".
Similarly, a commercial vessel may only need one HS of Engineering Spaces, but if I was designing a generation ship, I wouldn't include an 800-year supply of each and every screw and integrated circuit... I'd include fabrication facilities.
I'm not clear on why the mining platform has a fuel tank. I'm also not clear on why the mining platform and the fuel harvester have so much MSP storage - they're relying on the Unity for the interstellar trek, and as commercial vessels they don't need maintenance while in-system (presumably the Unity's Maintenance Modules won't be vanishing once they arrive).
I think the expedition could do with a small freighter. Something so the Unity itself doesn't have to worry about transporting facilities around. Possibly also a personnel transport.
I also think the expedition should include Infrastructure, just in case the destination doesn't have a habitable planet on arrival. Ten Infrastructure takes up the same room as a Factory, so it is a bit bulky, but provides habitation for all 50k of your colonists on a 2.0-cost world. If it's more costly, or worse a Low Gravity body, you do have the Orbital Habitat.
Instead of setting the Deployment Time so high, I'd include a Recreation Module. The crew gets places to rest and recuperate, not "new set of quarters every three days".
The expedition seems to be missing a ground force component. Not necessarily military, just Xenoarchaeology/Geosurvey/Construction trucks. Though a battalion of "security troopers" probably wouldn't go amiss, if there turns out to be particularly wild wildlife. As a bonus, 3200 tons (more or less) of Construction vehicles provides the same construction capability as 25000 tons of Construction Factory.