That is odd. I would have expected the older wood to be darker. So, as others have mentioned, I wonder if they used same species of wood. Or, maybe it was a different grade.
Anyway, no I would recommend against 2 coats of stain. That, IMO, is recipe for disaster. 2nd coat will not penetrate correctly and first coat of poly won't adhere properly.
I'm thinking a simpler and better solution is to screen & recoat the lighter section w/ another coat of poly...but add a tint to it.
Debbie Gartner aka The Flooring Girl
http://TheFlooringGirl.comOwner of Floor Coverings International
41 N Lawn Ave
Elmsford, NY 10523
Westchester County