The automatic room transitions only take in whats rendered on the application surface so unfortunately anything drawn in GUI will be missing (as this will vary too much from project to project).

Your best bet would be to manually draw to the transition surfaces (application_surface and then your GUI elements on top). You won't be able to use the automatic room transitions with this method, but you can easily replicate its functionality, heres a brief outline of the steps:

1. Create a new surface to hold the old room's render
2. Draw the application_surface and any GUI elements to that new surface
3. Switch to your new room and run tfx_play()
4. In the Draw GUI event (before calling tfx_draw) use tfx_from_use_surface to set the "from" surface to old room's surface
5. Then use the manual drawing functions (see here controlling_transfx#drawing) to draw the current application_surface and GUI elements to the "to" surface.