I've been launching Populous: The Beginning as software and it's been fine, sound is a little glitchy but it's manageable. I read that it came with the expansion but I don't see it anywhere. What am I missing or has it been taken down?

It should be called popTBUW.
I have it inside my folder C:\GOG Games\Populous - The Beginning look if it's there.
And didn't you get a shortcut to it?
Think it was supposed to be automaticly installed if not you were supposed to check the undiscovered world expansion pack when installing the game.

You bought the game here right?

I also bought POP3 but didn't get the UW addon :-(

For some reason it's not included in the gog galaxy version of popTB,
To get the expansion, you will need to download the game manually through the web client.

You mean thru Galaxy? When I look on the GOG product web site and click More -> GOG download links, I don't see anything more.

This may no longer be relevant but I downloaded the backup installer through GOG Galaxy and the expansion was in the downloaded installer. There are not two separate installers if that's what you're looking for; the expansion is integrated with the main game.

Hey ! i have had this problem too ) i found undescovered worlds game in gog galaxy

so steps to get this game :
1)go to gog galaxy
2)find your populous 3 game (click )
3)find (and click ) button MORE which near PLAY buton
4)find backups and additional materials (click)
5)find backup file of populouss 3 and click
after that game would be downloaded to direction what you choice
and that file would have populous3 and addon UW ..you need only to intall it and play
PROFIT ^ ^ ARATANGA lol