As a blanket rule, doing it all the time makes no sense, but it's note quite that simple.

If you know you'll have multiple runs to pull, I think three boxes is about right. Or imagine you have a box of a thousand feet and you know you need to make five runs of a hundred feet each in the same conduit (or along the same path). Pulling out and cutting four separate pieces of wire, a hundred feet long, is insane to deal with!

And if you're not exactly sure of the length, pulling from multiple boxes means you don't HAVE to work out the length before pulling anything.

Of course, this doesn't always work perfectly, but it's way better than pulling from one box.