I like this done, the decking tar papered, then the valley's tar papered going down the valley splitting the valley in half with tar paper.
Then it would not hurt to lay down flashing down the valley, but the flashing is compromised if nails penetrate the flashing. Most roofers realize this and will stop all nails when getting close to the valley or the flashing.
I think and feel that lacing is more labor entensive and will cost more than the cut line. But, whatever method you use make sure its done right.