Oh my ... You're giving too little information. Please tell more about your GPU, it's the main point of Linux CRT gaming.
Super resolutions do work, and you don't need to set any scaling parameter. The only ones that matter are monitor and modesetting.
But as you're on linux, why bother with super resolutions ? Don't transpose windows habbits on Linux, it doesnt work the same way. Linux can run at native resolutions (depending on your GPU, hence my very first question). If you must use super resolutions (this happens for GPUs that can't do low dotclocks : Intel and Nvidia mostly, AMD/Radeon do low dotclocks just fine), just set the min_dotclock to 25.0.
Now I'd recommend using the collaborative GroovyArcade OS. All of this is mostly automatically handled, and the bare minimum required patches are applied (Linux, SDL2). Otherwise, you need to compile your own kernel with some patches here and there, you're stuck with never updating, when GroovyArcade always has updated packages.