Hi Scott Stain normally doesn't seal a surface with a film like paint will. The reason you want to back prime any wood siding material is to keep moisture from going into the wood until it stops at the outside paint, thus keeping the inside of the wood moist most of the time as well as degrades the outside paint. It doesn't hurt to back stain but I really don't think it will matter very much.
FWIW; I helped my brother several years ago do this. He used a tall bucket with his stain, tapped a shingle nail into the bottom of each shingle and submerged each into the stain, hung to dry and then we installed them. He then applied a second coat of stain after we had them all up. That was about 12 years ago, and the shingles still have the original stain and still look fine. The only part about I really didn't like is I didn't get that nice cedar smell while we were installing the shingles :-)