You could add the command to your startup.txt in the save directory; if you own Nuclear Throne on Steam, openbeta_win64 (vanilla) and ntt_testing (NTT) branches both now have framerate and aspect ratio settings under Game.
Viewing post in v9940 - 60fps, chat revamp, mod stuff comments
I’ve been on and off working on the game itself since 2017 - update 99 and the (slightly unfortunate) Xbox port are my work, as is the ongoing effort to migrate the game to current GM versions.