Both works well. Valleys are the most likely areas to leak when a leak will occur.
I would use flashing and have it on my roof. However, like any valley material, do not puncture with a nail. Know at all times where the flashing is located.
I also recommend to roll two strips of #30 tar paper down the valley also. Tar paper is much cheaper than roll shingles.
Good Luck RUFF RUFF
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