Disabling the background should never have made anything transparent in the normal render output, as far as I know. The only way to get transparency out is with a render Alpha. The alpha is in a separate image, Terragen doesn't support embedded alpha. You can either switch to Alpha in the Renderer view after a render is completed and save that separately, or access it in the Render Temp files if you have that enabled, or use Extra Output Images and Render All To Disk on the Sequence/Output tab of the Renderer.
- Oshyan