asymmetric spindle wrong way
 

I just got into my possession a 1987 (or 1988? s# is 309256) Trek Elance 400 and quickly noticed that the bottom bracket spindle was longer on the non-drive side than the drive side by about 5mm. never having encountered such before, I just assumed it was wrong and so flipped its orientation while I was repacking the bottom bracket. the chain line was obviously amiss at that point, and so I put the spindle back to its original orientation and was left scratching my head as to why Trek would use an asymmetric spindle when they didn't need to, considering they had to orient it "backwards" to make the chain line correct.

Is there any particular reason this may have been done on this particular Trek, besides my initial thought that they had a surplus of spindles of this size that they needed to use up somehow. yeah, I am also making the assumption that this is the original spindle that this bicycle came from the factory with.

You my not have gotten far enough to check left arm/chainstay clearance, but that's one possibility.

Consider also that the total crank offset is based on the spindle length and the offset built into the cranks. If the right arm had more built in offset, the left side of the spindle would be longer to compensate, so pedal Q-factor was equal on both sides.

There could be other reasons including the overstock issue you mentioned (though I doubt it), but be aware that spindles longer on the left aren't all that rare.

Did you check the Q-factor before disassembaly? It is possible that the wrong spindle got pulled for your particular build and the assembler did what they could to get the correct chainline.

My 1993 Trek 7000 MTB also came with the bb spindle installed the "wrong" way, i.e. the longer side to the non-drive side. When I tried to correct this "mistake" the non-drive side crank arm hit the left chainstay so it was done intentionally.