@XtraSmiley
No need to worry about the square being filled or not. That's just my scanline settings. You can make them literal perfect squares if you want assuming it's dialed in correctly. The big thing I've learned about sample rate is that it's more about where each pixel lines up on the screen rather than the shape of them so much. Too low sample rate will get you pixels too far apart and outright missing information. Too high will cause overlap. I believe this is because in a sense "too much" information was gathered as seen in the pictures above.
Here's a great video I found explaining sample rate:
View: https://www.youtube.com/watch?v=nLmB1qcXT4Q
Here's another photo to show a misaligned sample rate:
It's not the shape that's so important here but where the pixels are placed. There's supposed to be a clear black gap between each vertical line. You can see it correct on the left and right side, but the middle is all messed up because the sample rate is too high there and it's putting additional blue and green pixels where none should exist. A correct SR would fix that and make it completely uniform.
Here's my settings I'm using. I'm on a 2 player Japanese PCB but that may not matter. You may need to slightly adjust your sample rate differently than mine but it should be very close if it's not exact. I used the cross pattern in the test menu of the game to help dial it in properly since it does a good job showing the flaws especially when the scanlines are on.
By the way, to clarify. Although I'm passionate about getting pixel perfection for my games, that's me. If other people want to use other settings that aren't "pixel perfect" or whatever, that's fine. I certainly don't wanna sound preachy about it. It's video games, just have fun