Different cranksets sit in different places on the taper of the spindle. You would think that all would sit say 14mmm onto the taper so any two cranksets would sit it the same place with the same chainline. One would think two countries separated by 12 miles of water would use the same bottom bracket threading. (English and French. They cannot even agree which direction to thread the cups. One would think the bicycle industry would get itself together and create standards. (Scratches head.) But they have! Dozens of them! There are standards to fit any possible application(/nationality/units system/you name it).

rant, rant. But you get the point.

And then there is the fact that square taper cranksets tend to sit progressively further in as they get re-assembled. Sometimes so far that the crank starts to hit the chainstay and therefore now requiring a longer spindle (or shims or the bottom bracket cup needs a washer to space it out).

Ben