Thanks for the tips. I followed your advice, and then did some testing of my own. I have a 1080 and a CV1.
I've found that if you really want to improve image quality, you need to use a combination of supersampling and anti-aliasing (FXAA or SMAA). Either one alone will leave extra jaggies. The AA costs about a 5% performance hit, but if you have the headroom, it may not decrease FPS in some situations.
The in-game supersampling and the debug tool have the exact same effect on FPS. So the main benefit of the debug tool is for values between 1.0x and 1.5x supersampling (you want to use something over 1.0x to reduce jaggies). I suspect they use the same algorithm.
If you use a large value in the debug tool and a low value in-game, there is a performance hit in FPS. You may not notice this in space, as it may be locked at 90 FPS, but you can see a difference in stations, on planets, and in combat. For example, if you use 2.0x and .65x (which equals 1.3x), your FPS in those situation may be about 30% lower than just using 1.3x and 1.0x (which also equals 1.3x - no duh). And as far as I could tell, the image quality looked identical. Btw, it seems that the larger the debug tool multiplier used, the more pronounced this effect is, so using 1.75x and .75x may only be a 10% reduction if FPS.
So if you are using in-game downsampling, you may want to try this - ymmv. [yesnod]
Note: all testing performed in an underground small hangar with default ultra graphics settings and ships lights on.