At least in mathematics, the arXiv is a pre-print server --- papers are mostly eventually published, and receive DOIs then. In fact, the arXiv encourages authors to add these DOIs to the arXiv metadata when they become available.
I think it could be quite confusing for papers to end up with two DOIs. Given that the arXiv numbering scheme works quite well, and in practice everyeveryone knows how to resolve handles of the form arXiv:NNNN.MMMMM
, why add the complication?