I just want to make sure it's the PC version

It´s the Windows version, not the N64 one.

which is the difference between the PC version and N64?

Some differences I could notice regarding the PC version...

- Has FMVs (intro + endings for each character);
-- BTW you can skip the intros automatically by going into the "movie" folder, making copies of "black.smk" and renaming these copies "Intro.smk", "Kronos.smk" and "Vtokai.smk";

- Has voiceovers (instead of green scrolling text);

- Better audio quality (sounds less muffled);

- Worse graphics by a long shot...
-- Missing texture filtering (blocky jagged edges everywhere);
-- I'm not sure but it might have lower texture resolutions;
-- Missing the parallax layering in backgrounds;
-- Missing the fade between the floor and background;
-- Missing dynamic lighting/shadow effects on fighters (shadows are just blobs instead of projections, and the lighting/shading on the characters is permanently baked onto the textures);
-- Hit effects are flat 2D sprites;
-- Much simpler overlays (like the "BATTLE COMMENCE" message and pause menu);
-- Fighters have lots of stray transparent pixels in their textures;
-- Morphix's textures look rough and don't animate as fluidly, probably missing some transparency and shine effects;
-- Life bars are rendered in front of the fighters (instead of behind);

[I've attached a quick comparison between screenshots, N64 on the left and PC on the right.
Don't mind the screen sizes, I just took these haphazardly to transmit the gist of the differences.
EDIT: wait, GOG sent my attachment to the shadow realm, here's a link: https://imgur.com/a/o6lBlBz ]

- Main menu displays all options vertically (instead of a single one at a time);

- No practice mode, apparently;

- Either it doesn't have "Vs" and "Prepare for battle" screens or it just loads so fast I couldn't see them;

- Weird speedups here and there;

- Sometimes it doesn't let you pick a character and just gives you the first one;
-- Using the kick button to pick options in the main menu seems to fix this I think (?);

- Kinda unstable. It may not run depending on other programs you have open, and sometimes it just randomly refuses to launch.

Mind you, there's a chance that some of these may vary depending on your computer and how you run it. I just used the vanilla GOG files and configs (which use DxWnd by default).
But overall it just looks like an unfinished PS1 version. I think I'd stick to the N64 version anyway.

Also if you can, check Cardinal Syn on the PS1, which is another cool 3D fighter Kronos made after this one. Avoid Criticom, though, that one sucks.