I played the original version when you released it, and enjoyed it. We were really busy at the time and I didn't have the energy to write up my thoughts into a coherent comment. When I saw this in the jam I was looking forward to checking it out and seeing the updates.
I like the tutorial. It does a good job of teaching the game and letting the player have freedom to design their base. The map is a good size allowing plenty of freedom to pick a spot that works for the player's vision. Having the last step start everything into motion was a great design choice. One minor thing on the tutorial. When you get to step 9/9, the button still says "Skip tutorial". I'd change that to "End tutorial", or similar.
The hover text on the transporters mentions carrying finished parts, but not transporting the ore to the factories.
When a ship is fully assembled it plays the same sound as for a countdown, but beeps only once. That does draw attention to it, but I think it would be nice if the sound was different. It makes me think it is starting the launch countdown. The main countdown is plenty of time to get back to watch the launch, but I do like the heads up when it is assembled. I'd just prefer a different sound so I have a more clear idea of timing for when I should scroll over there to watch, especially when there are multiple pads.
On the upgrades screen, I was wondering what the "FIT" button did, as nothing happened when I pressed it. I was starting to comment on it when I finally noticed the small text at the bottom about panning and zooming the upgrades screen. I've never felt the need to zoom or move things, as everything fits just fine and is readable for me. If yo continue to expand the tree I could see that being useful. I think the zoom/pan informational text needs to be more visible. Being so small, and over the main UI buttons, makes it easy to miss. It could be placed in a Panel Container with a different background color of its own, or maybe have the text be brighter white. Moving it next to the FIT button could also help connect them. This isn't a huge issue, but I kept wondering about that button every time I opened the screen. A tooltip on the button would also be a good choice.
An accessibility detail here. It would be a good idea to have an option to turn off screen shake. That can be problematic for some people. It was only a minor annoyance for me when I went to place a new Launch Pad and things were shaking so I couldn't get it where I wanted it. A general option for it in the settings is what I was initially thinking, but a nice extra would be if you could hold Shift, or some other key, to temporarily disable it while placing things, especially if you have a lot of rockets going off.
I got every upgrade but Heavy Lifter before the last group of the initial colonists launched, and I sat on the upgrades screen to get it as soon as the points were available, which was just before the Congratulations popup showed. I had 4 of each building. I had 5 Excavators. I think I had 6 Transporters, but they were moving too fast to reliably count them. It would be nice to show a count somewhere. A game like this can always use more stats and details! Similarly, it would be nice to have a score, or overall stats screen when you win. Something like totals of everything mined, built, accumulated. Maybe include how long it took. Something you are probably not tracking, and I'm not sure it would be worth the effort of doing so, but might be fun, would be distances traveled. How many steps did the colonists have to walk to get to the launch pads? How much distance did the Transporters and Excavators cover?
A nice to have control would be using the middle mouse to drag the screen around.
I've enjoyed playing Star City. I do like Sci-Fi and builder games. It is simple and short, so works well for something I can play to relax, and also not feel like I'm going to be sucked into hours of playing when I should be working (or getting some sleep), at least in its current state ;)
Reading your devlog, I like Rootwarden, but fully understand the need to step back and try other things sometimes. We also had some projects we thought were going to be our big project, and then found we could not make our vision work for a full game with where we were going and our skills of the time. It can be easy to get yourself in too deep and locked into a certain direction that things just aren't working. Maybe after stepping back and working on this it will inspire you with new ideas for Rootwarden, or something else you want to work on more.