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
• GlideN64?
• probably others ... don't really pay as much attention to plugins as I used to

Does the current PJ64 support Star Wars: Battle for Naboo?

Not without the fixfpulocations hack.
https://github.com/project64/project64/pull/251