These warnings are way overstated. I don’t know what GOG’s setup is like but I’ve played this on DOSBox loads of times without any real difficulty. Bottom line is run it at a fixed cycle count of around 3000-4000 and you will be fine. If you really need to, use ctrl-F11, Ctrl-F12 to change the speed a bit.
Wing Commander never ran at 60 fps. It simply wasn’t all that smooth in the first place. I think the main problem people have is that they crank up the cycles to get it running smoothly and it goes into fast forward.
With real hardware, it should run fine on a 486 or Pentium if you switch off the CPU caching. The ideal platform is something along the lines of a 386-25.
Whatever your platform, I would strongly advise playing this with a joystick. I suppose it should be playable with the analog stick on a controller either. I really don’t advise using keyboard or mouse.