The tracker originates from Europe (mid 80's Amiga scene) and has never been widespread outside of the European scene until much later, as far as I know.
In any case: You should look into specific developers and their sound engines / development kits if you want to know exactly how those soundtracks were made. You also have to know about different methods of sound synthesis and which chips are fitted in what systems. Super Famicom's chip for instance, was purely sample based (recorded sound), while Mega Drive used a combination of FM/PCM and PSG. These are wildly different means of producing sound.
Some of the development kits were MIDI based, but often they had to code by hand (no dedicated music software at all (like trackers), though in some cases with a simplified music language, like MML). There are also cases were composers who wrote the score in a MIDI environment first (or even music sheets) and then let a programmer do the sound design (by coding the music for a specific chip).
As for composing for old systems today, there are often many alternatives. Just google away, find some chip music community or whatever.
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