Make sure to use the switch version in the download link, and use the full memory access override or the game will fail at loading screen:
https://gbatemp.net/threads/use-atmosphere-to-access-full-ram-with-homebrews-without-nsp.521240/
It won't recognise the joy cons in their sideways mode, however, it is still achievable (ish):
Load the game normally - (use full memory access).
press the home key to go to switch menu
go to switch controllers and register player 1 in sideways mode.
return to openbor game
activate the second joycon
Use the openBOR controller config menu to configure the the buttons so you can use it in a sideways fashion. So effectively it's not sideways mode it's:
player 1 = joycon-1-left
player 2 = joycon-2-right.
However, you won't be able to use the SL and SR shoulder buttons as it's technically not sideways mode, however, it does mean that L+ZL is available for player 1 and R+ZR for player 2, just inconveniently placed I guess.
To quit OpenBOR use switch home menu button and close application.