I've finally come to the end of my research trail for this issue.

I have PRACX installed and am playing Alpha Centauri on a Dell Venue 8 pro with 1280 x 800 resolution. When the game is full screened the main menu and the in game menu are both scaled too large for the screen. alt-enter switching to windowed mode makes the UI scale properly, but no full screen options fix the issue. Changing desktop resolution, or using the screenheight/screenwidth options in the ini under the PRACX section will change the resolution as expected, but the ui continue to be incorrectly scaled.

The simple DirectDraw fix also doesn't scale the menu to the top of the base window is cut off, making changing production impossible.

Is there any way to fix this, or am I simply stuck playing the game in windowed mode?

I found the solution. The creator's update for Windows 10 only has an overall "scaling" setting for everything. I had it set to 125% which scales the Alpha Centauri UI, evidently. Setting it back to 100% fixed the issue.