N64 depth compare is incompatible with MSAA. If MSAA is set to anything other than 0, it should be disabled and if N64 depth compare is enabled MSAA should be disabled. Tooltips likely should say "incompatible with N64 depth compare" or something if it's disabled, the same for depth compare saying that for MSAA if it's disabled.
N64 depth compare fixes issues in most games. Usually this is regarding shadows, lighting or various clipping problems. It should be defaulted to On for accuracy (but also could have potential hardware requirements).
In Frame buffer settings, under the tick for Use defaults for current game, set Copy Depth to RDRAM to "Use software renderer". This fixes lens flares in Zelda games, Banjo games, etc. It probably fixes lense flares in all games. Without this, they're rendered on top of all geometry. This should likely be a default setting for emulation accuracy for all games for accuracy, unless otherwise specified per game.
Similar to the above, in Frame buffer settings, under the tick for Use defaults for current game, set Copy Color to RDRAM to "Copy in Sync Mode". This is the most compatible option for games.
Bilinear filtering should be set by default to to "N64 3-point" for accuracy.
Also there should be some more encouraging text that it's preferred for TASing maybe.