I tried loading 5200 games prior to having the the correct Atari ROMs in the /home/pi/RetroPie/BIOS/ directory.
So I'd like to pitch-in, hoping this can help others. Gamepad still not working, but at least games are now loading) I had the same issue and I finally managed to get Atari 5200 to work. I am running a clean Stretch beta image, updated to version 4.3.16, on a Raspberry Pi 3 B+. If anybody can help me out, I would greatly appreciate it :) I don't see any documentation in the wiki on the new lr-atari800 emulator. I first searched the forum but did not find an answer to this. My question is, how can I get it to just launch an Atari 5200 rom from EmulationStation and go directly into the game without displaying the blue 'ATARI COMPUTER - MEMO PAD' screen and requiring keyboard inputs? The game then runs perfectly with Libretro controls. I can however at this screen hit F1 on a keyboard, select 'Run Atari Program', then navigate to and select an Atari 5200 rom from my rom directory. At this screen, the only thing I can do with a controller is press SELECT+START to exit back to EmulationStation.
When I launch an Atari 5200 rom in EmulationStation using the new lr-atari800 emulator, I just get a blue screen that says 'ATARI COMPUTER - MEMO PAD' at the top.