this is one reason why MOD Plug Tracker XM/IT files are incompatible with other Trackers/Players that read XM/IT files: Mod Plug Tracker lets you use true stereo samples. i did a lot of that until i found MPT was the ONLY program that played them properly. i've moved onto Renoise which lets you use stereo samples natively.
when working on other trackers like Milky or Fast Tracker, i've used the technique of panning left and right two identical notes and offsetting the timing slightly to emulate the disparity our ears experience in receiving a sound at two different times (very tiny difference in the time a sound gets to one ear compared to the other - the space between left and right ears is small but enough for each ear to receive the sound at different times - it gives us a sense of depth, that's how human hearing works - it's called "binaural").
when i want to use a stereo recording in a tracker not supporting stereo samples, i do what was mentioned above: two instruments. one for left sample. one for right sample. panned hard left and right, respectively. ensure that the notes are triggered exactly the same time. you might need to take your stereo samples and split the left and right portions into separate files to load into the tracker. you can do that with an editor like Sound Forge, or just import the sample two times (choosing different channels each time when asked what you want to do with the extra data the tracker can't use).
as for VSTi and hardware synths... lots of what you hear as "stereo" are effects applied to the output. chorus, delay and reverb (which are all forms of delaying one signal in the left and right set, anyway). lots of old synths sound "bad" to us today because they didn't have effects. in the old days, you had to add those in the recording and mixing process with other dedicated equipment. MODs are a bit like that, in a way.