How to Fix
First, it runs on Steam Deck no issue. I did proactively set it to run in windowed mode via the launcher based on other posts here, but that was it.
Now, when the tutorial tells you to build a housing or city district, the tutorial window blocks the build button and cannot be moved or closed. The workaround is to either open the keyboard and press “b” or set a button to “b” and press that. That is the hot key to build the selected district.
The second, and thankfully only other serious issue is on the same world screen when it asks you to close out the window by using the the “X” in the corner or escape key. The tutorial window blocks it. Similar solution as above: because there’s no escape key on the keyboard, you have to set a button to escape and press that.
At even max resolution (1280×800), the empire selection screen shows no empires to select.
Set UI scaling to 0.8 and that will show them. Select, save, reset UI scale to desired, and viola!