-autostretchxy should be set back to 0 when you're using a CRT.
I believe your card has at least an analog output? If so, you don't really need to use super-resolutions -- that just helps to have it all working faster and keep the installed video modes in lower quantities and the per-game horizontal amplitude more uniform. Using the native resolution modes will be more authentic since you may find some minor artifacts with super-resolutions and non-integer horizontal scaling, but you'll lose the seamless resolution switching for the games that do it, as explained in the guide. In practice, many consider this splitting hairs, and you can always set a general super-resolution and later make a per-game configuration for the cases you prefer for whatever reason.