We could go into computer forensics if you want. However on balance of probability then they made a version of the code that compiles to byte for byte the original game, warts and all. Even if they had a 1000 strong team that did it full time since the original game was released back in the 90s the chances of that happening are so minute as to not even be worth considering. I would be impressed if they could do that for windows 3.11 minesweeper with the same provisos, never mind a complicated 3d world game for the N64 that has such random functionality as is described in the following sorts of videos
Two people write the same short story, song, poem, take the same photo... there could be some doubt. You get to ask for earlier copies, whether they crossed paths, whether one could have been influenced by another (same location around the same time), whether it is based off an earlier work of some form and is an obvious change... usual copyright case stuff.
Two groups write the same thousands and thousands of lines long code for a complicated game that compiles to something exactly the same as another. Forensics at this point is basically academic**.
If said thousand strong group had started back in the 90s, limited themselves to static non code analysis, maybe some cheat type memory viewing and the like then they might have made a functional clone that plays basically the same as far as anybody cares; there are what 30 moves really, a few dozen enemy behaviours you could map from video, including non linear acceleration, you could do some kind of unit test for camera to divine its behaviours (personally I would want to make them better,
https://web.archive.org/web/2016051...loads/332-aim-assist-cameraReady-v8-final.pdf https://docs.google.com/document/d/1iNSQIyNpVGHeak6isbP6AHdHD50gs8MNXF1GCf08efg/pub?embedded=true , but maybe we are deliberately cloning and not straying), quarter frame position checks is a bit outside the box but not that unreasonable when playing with floats, 3d level layout will follow one of a handful of formulas* that look obvious when you know what to look for, you could probably track or trick any 3d effects to not showing up (see various graphics based cheats in all manner of N64 games from wireframe to no textures to whatever else) and calculate differences... even with all that then a functionally identical (which is radically different to byte for byte in something this complicated, indeed it would be impressive for tic tac toe/noughts and crosses) it would still be a massively impressive project. All the things covered just now would also be the general theme of a clean room project, and if it sounds horribly long winded and tedious then yes, yes it is.
*basic 3d model, model of "track" as you want to control behaviours without having to calculate 3d collisions all the time (more prominent in racing games as a concept hackers care about; see mario kart kcl files if you want a reasonable start in such fields), powerups/interactable objects, animated objects, enemy placement/spawners... might be all in one, might be 3 major ones as seen in a lot of 2d games, might be all five or spun into even more. Each of those is likely to be one of of the two major 3d model approaches (bones and vertices, the victor tending to be picked based on the hardware the system uses that you could reasonably know) or some flavour of coordinate system.
**though actually as 99% of stuff here we ever see in court cases is "you used this open source project and we can prove it from the code", "you used this leaked code/specification and we can prove it", "you copied these lines from this as it has the same bugs*** we had that nobody else would have programmed in" and "you took this code when you left the company and we can prove it" then it might actually be somewhat interesting to ponder.
***concept going back to maps
https://bigthink.com/strange-maps/670-nil-how-to-hide-an-elephant-the-1923-gold-coast-survey video on similar matters, the telephone directory cases are another popular one for this
https://supreme.justia.com/cases/federal/us/499/340/ , and seen somewhat recently when it was shown google was scraping lyric websites
https://www.masslawblog.com/contracts/does-genius-have-an-illegal-scraping-case-against-google/