Very small, subtle differences AFAIK. Only evidence of difference (aside from episodes) which I know are the version numbers (press V inflight) and Locke's infinite ammo patch had to be updated for the different SO versions.
BTW, all the episode executables did was update the MISSIONS.TRE, overwriting the old file. Naturally, the Gold version already has all the missions. So I assume there's no difference in directory structure or whatever else you're concerned about.