Today I redownloaded the game because of the Undiscovered Worlds Update.
Now I'm facing several issues that I didn't have with the previous version.

When I'm trying to start the game via the shortcut, it shows me the error "D3DPopTB.exe cannot be started", which another user in the forum already mentioned.

After that, I lokked in the start menu, to use the setup for the game, like I did for the previous version, but all I could find were the game shortcuts and the uninstall option.
So I looked in the game folder, but a Gogsetup or the like were not there.

Then I used the game executable directly, which made the game launch (the D3D version), but gave me messed up colours in the menus.
Also I couldn't set the resolution higher than 800x600, which is given without the setup.

Hope somebody can help me with this issue or is atleast experiencing the same so I know this is not a local problem.

I have exactly the same problems.

I think the "GOG Launcher" thing cannot launch the game for some weird reason, but it is possible to edit the shortcuts and launch the game directly from game files. In my case:
"D:\Gry\Populous - The Beginning\D3DPopTB.exe" (base game, Direct3D)
"D:\Gry\Populous - The Beginning\PopTB.exe" (base game, Software)
"D:\Gry\Populous - The Beginning\D3DPopTBUW.exe" (expansion, Direct3D)
"D:\Gry\Populous - The Beginning\PopTBUW.exe" (expansion, Software)

It works for me. If Direct3D gives you messed-up colors, you should try Software.

My PoP3 game has the same issue too. The GOGSetup.exe file is missing and I can't adjust the resolution.

You saved me!