When it says stuff like that in Project64's browser, it isn't really paying attention to what plugins are selected. They're just hard-coded notes complaining that the default "first-party", official setups were not designed to support those games.
As for what graphics plugins do support them, basically anything with LLE video.
- Jabo's Direct3D8 1.7+ (not 1.6.1 or earlier)
- z64 and z64gl ports of MAME
- Per-pixel software graphics renderer maintained by angrylion
- probably others ... don't really pay as much attention to plugins as I used to