With a simple ini tweak you can access your Atoms or Fallout 1st membership with the Steam version of the game.
How to access your Atoms from Bethesda Launcher on Steam
Simply go to “Documents\My Games\Fallout 76\Fallout76Custom.ini” and add
bSteamEnabled = 0
Now when you launch the game it will ask you to login and that’s it!
If you don’t want to enter your Username and Password every time you can also add
Of course you could also just spend your atoms, set bSteamEnabled = 1 (or delete it), and go back to Steam. Whatever you choose do, the option is there. Not exactly sure why Bethesda didn’t just transfer the Atoms in the first place but not like it matters much.