As with most of these decomps there is no copyrighted material included in the link and you have to provide your own ROM (and a very specific version of it) in order to build and get it to work.
After that I believe I just copied the folders to the Deck, mapped it as a non-Steam game, added updated artwork with the steamgriddb plugin etc.
I might have messed with the controls a bit but I don't recall. There is probably a more detailed Steamdeck-specific guide somewhere if you care to dig.
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.