i would recon this is true more often than not for attempts at 1:1 ports. glitches are more often introduced than fixed in the porting process, so if it isn't deliberately a remaster or offers extra content, you're probably better off with the original in an emulator. if you're interested in mods, it's also worth thinking about where the reverse engineering efforts have been focused- a lot of native PC ports have been picked apart and put back together with bugfixes and new content after the fact
sonic adventure is an example of all of the above. if you want the absolute worst version possible, just buy it off steam. if you want the best version possible, buy it off steam and mod the shit out of it. fan efforts to fix an abysmal port of a port ended up creating an experience that arguably surpasses the original before even getting into all the extra bells and whistles you can mod in
fan ports are also increasingly becoming a thing, so i guess the moral of the story is this: as far as official offerings go, emulation is probably going to be better than a native port, but if a game has enough enthusiastic hackers, then they may have frankensteined something even better together