It seems I was wrong about HPLL2x not being used in the optimized mode. When Marqs was working on fixing the unstable optimized modes he removed HPLL2x from the optimized modes but I missed that he put it back later. Not sure why though since it was the cause of the unstable optimized modes.
Higher lpf values means less filtering. With video lpf off you may see noise so you should mostly just leave it on Auto. It was recently found that the THS7314 amp used in SNES/N64 mods already has a lpf so you should set Video lpf to off in that case. But with N64 I also didnt see any difference with video lpf on or off so I just leave it on Auto.
For sync lpf I always leave it at 2.5Mhz max because otherwise it might lose sync in some cases. You won’t see a difference except that the image might shift horizontally.