Is there a reason not to have bones with overlapping positions?

At my current company their skeleton has a lot of overlapping joints ( spine starts overlapping the hips, first upper arm twist overlapping the shoulder, etc) .
When the skeleton is characterized in Motionbuilder, it throws warnings about overlapped joints positions, but you can still do everything nevertheless I would like to have a clean file.
I had a look over the free Paragon chars and they have small position offsets for the shoulder / thigh twist bones so i was wondering if there a specific reason not to have bones with overlapping positions in a skeleton?

Everything should work relatively fine. The only reason I can see would be that weight painting/rigging could be more difficult. You may also run into problems if you are trying to use animations made with the UE4 skeleton.