Okay, instead of using viewport zoom for this, you could try using Non-Integer Scale %. There should be a point where it goes away.
Seeing that you got it to go away by using Integer Scale Mode, you can switch on Integer Scale Mode 1, then in the Shader Parameters turn on Show Info. It should be the first option in Shader Parameters Menu.
Look for either Integer Scale % or Non-Integer Scale % here. Take a note of that value, then change Integer Scale Mode back to 0. Then enter the value you got (or as close as possible to it) in the step before as the Integer Scale Mode %.
It is very likely that that the “phenomenon” might be reduced, gone or different. You might have to fine tune the value until the anomaly is gone.
The reason I used Non-Integer Scale instead of Integer Scale in this instance is that PSX games that change resolution change the bezel dimensions as well and I find this to be a bit distracting.
Of course you’re free to use whatever Integer Scale Mode works for you.
Also remember that I use Mask Layout = 1 for my 1080p Optimized presets. You should choose the Mask Layout that’s appropriate for your display.