Yes, you can create a flight over a landscape. The animation version allows you to animate nearly any parameter of any node, object, etc. It's very powerful.
Animated Terragen files have exactly the same extension as non-animated - TGD. But I realize that's not really answering the root of your question. Terragen would output a series of image files of an animated sequence. You would probably then use these as background in either your other 3D program, or in your video editor/compsitor, to create the final result. Future versions of Terragen will be able to output additional rendered scene data such as alpha channel (already supported), depth map, motion vectors, etc. which you can use in a compositor or advanced video editor to better integrate other elements.
Alternatively, or in addition, you could export the terrain from Terragen in OBJ format using a micro exporter, then load that into Maya to create and render your animated elements. You could front-project the Terragen rendered elements over the terrain to do "compositing" within the Maya render, or render out the Maya elements separately and composite them in your video editing process.
In the future, FBX will be supported and you'll be able to import and export animation information, but it's critical to understand that that doesn't mean you will be able to get Terragen-like data into Maya or vice verse. The data interchange is best used as reference for syncing up motion, and for things like shadow catching and whatnot (so your objects can properly cast a shadow onto the terrain shapes). If you output separately rendered elements from each program, you'll have maximum flexibility to composite it all together later.
- Oshyan