I'm curious to know what it's using to run on modern systems?

I haven't bought the GOG version (yet) but I have a genuine original POD 1.0 CD, which I can install the 3dfx version of, then update with several official patches, and finally use dgVoodoo to run. This works, although it tends to lock up when exiting the program, and sometimes does weird things to my mouse.

Is the GOG version superior? Does it use a different 3dfx layer?

It is using GOG's Glide wrapper, but it is better to use nGlide and remove GOG's glide2x.dll instead.

I don't think GOG's version is superior to the CD one, but it is POD Gold instead of POD 1.0 so you don't have to go through patching it manually. All you really need is nGlide and maybe nico's Podhacks to fix most issues.

Sometimes it still crashes on exit no matter what, I find using alt+f4 at the menu avoids it.