Inside a 3 jaw chuck there is a threaded plate. On the jaws there is a thread that mates with the start on the threaded plate. Putting #1 into #3, then #2 into #1 then #3 into #2 locations will cause the jaws to close in an odd pattern and not clamp properly.
Now, would is be OK to put #1 into #3, then #2 into #1 then #3 into #2 while making sure the #1 jaw starts first, then #2 jaw starts second and #3 starts third? I don't believe it would make any difference. I have always put #1 into #1 and never violated that, so, I do NOT know for sure. I do know how the chucks work as I have worked with them through my career.
As to balancing, I don't believe chucks are balanced with jaws in place. That would mean you would never be able to swap out jaws with different jaws. I have mounted a hugh variety of jaws on a lot of different chucks. Chucks on wood lathes are no different.