there are many reasons, i'll name the ones i know off the top of my head with my limited knowledge
lubrication: when you spray lubricant on the chain, you aren't gonna lubricate every part in the same way
when riding, dirt, rocks etc, the chain isn't gonna get dirty all over the exact same way... thus further uneven wear
you should look up the topic if you're interested, i got interested a few years ago when i noticed tight spots in my Ducati monster 620 and did some research about it. there is some bad info online but good info too... i'm also lucky to have a few mechanic friends that always help when i have questions etc....
also, notice, almost every motorcycle manual will say "mesure slack the tightest spot" because it's nearly impossible to have without tight spots