Broadly speaking, ray-tracing is a graphic rendering technique that produces more accurate light reflections (and realistic looking graphics) but is demanding of rendering hardware and therefore associated with modern games and consoles/PCs.
The project I linked is a decomp specific to Perfect Dark that uses existing ROMs. Basically it builds you a standalone runnable Perfect Dark with more modern enhancements, but I don't think it supports ray tracing.
The project in the original Tom's Hardware article appears to include a separate tool that is generic and could potentially be used on various N64 games with user-supplied ROMs. I don't see a list of games that are supported so I can't speak for Perfect Dark.
I know there are raytracing plugins for n64 emulation but I'm not sure which Retroarch core and settings would support that. Probably requires experimentation to see what works and what doesn't.