Few months ago, GoG updated their install with DDrawCompat. Which is set to "borderless".
The ini file is in the Apps folder wherever you installed SC3k.
It has:
FpsLimiter = msgloop(45)
FullscreenMode = borderless
SupportedREsolutions = 640x480, 800x600, 1024x768, 1280x720, 1360x768, 1920x1080
LogLevel = none

This is used because it includes a bunch of features, including FPS limiter (required with SC3k from my past experience). And borderless so less crashes for those who stream/record (I do not care, others do of course) and/or alt-tabbing.

Anyways, about the most you can do is tell Windows to hide the taskbar and wait for it to hide itself BEFORE starting SC3k. You may still have a few pixels at the very bottom below the screen though. (This was tested on W10 with 1080 monitor)
I tried adding the RemoveBorders option did not do anything.
I tried changing borderless to exclusive but didn't change behavior.
It seems SC3k does not quite support doing borderless correctly, as the top bar is still there (can't interact with it though).

There is a newer version of DDrawCompat:
https://github.com/narzoul/DDrawCompat/releases
Nothing in there sounds like it would fix this. (Tested, did not fix)
Other settings if you want to mess around in DDrawCompat:
You can hit Shift-F11 and change some settings, otherwise the ini file has to be modified directly.
https://github.com/narzoul/DDrawCompat/wiki/Configuration

An alternative is to replace DDrawCompat with dgVoodoo, making sure to turn dgVoodoo FPS limiter on (to 45) as well. I have not tested this.

Eh, just tested dgvoodoo, and doing the same type of thing. Only choice is set resolution to one smaller than your max on monitor, or have Windows autohide the taskbar.

What makes no sense is it was working fine ealier in the same day and for the last several days. I was playing the game just fine for several hours, stepped away for several hours, and when I came back I ran into this windowed problem.

Unless I am misunderstanding, borderless is actually what I want, where I can't see or interact with the desktop at all. Until this sudden incident I could not see the desktop nor the windows bar. The game behaved as if it was full screen. Now it's in a small window where I can see tons of the desktop and if I try to scroll the screen I "move out of the game" and it interacts with the desktop, and if I increase the resolution to cover the entire screen the bottom inch of the UI goes below the windows bar and off the screen (even with the windows bar hidden). The game is unplayable now.

EDIT: Looks like uninstalling, completely deleting what was left in the Sim City 3000 GoG folder, and then reinstalling fixed the issue.