Mmmmm, mine fills the screen, try:

Editing the es_system.cfg file so that for the Atari 2600 <command> it reads runcommand.sh 2, arther than runcommand.sh 1

The 1 makes it go to VGA whereas the 2 keeps the existing resolution.

And set your TV Pictue Mode (or equivalent) to 4:3 ratio

Those two changes worked for me !