The variations are endless. Long ago and far away I spent a considerable time one day trying out a dozen brand new Gibson Les Pauls. I didn't really care for any of them but some of them sounded like a wet log and others had more sustain and clarity. I didn't analyze them to figure out why but they were quite different. There could be many reasons for it.
One reason is where the wood was grown. Wood close to a river absorbs more moisture and becomes a heavier, denser wood, Wood grown on a hill is less dense. This difference is significant enough that at least with the "old" Gibson, the wood that was grown closer to a river was considered more desirable, and used in the really high-end guitars.
And there are also variations within the guitar itself. I've often written about how changing pickup height in relation to the strings alters sustain. Also, I remember touring the PRS factor with Paul. He would go past blocks of wood and "ping" each one to check out the resonant qualities. I find PRS electric guitars to be very "alive," even when not plugged in.
Any one difference is probably not that great, but when you add them all together, they give different guitars different personalities. I often find myself reaching for specific guitars to fill particular roles in specific songs. Playing the same part on a different guitar just doesn't produce the same result.