My TV has no options like "Full Pixel". I also noticed that WinUAE produces these "scaling lines" if you don't set it to full values, e.g. 1.5 Horizontal Size/Vertical Size 3.0. There are still vertical glitches in horizontal scrolling (not all games, Universal Warrior is an example), but no more in vertical scrolling.

That's cool. Actually thinking about it, if Windows looks perfectly clear set to that resolution then it must be mapping pixels 1:1 anyway.

I have to turn the option on with my TV otherwise it overscans so the desktop is larger than the display area (and blurry). But I am using an HDMI cable which may be a reason I guess.