How can I blend sanded cedar into the surrounding darker wood with a polyurethane finish?
Wood naturally changes color over time and it looks like your cedar material was no exception. When you sanded the material in some spots you sanded away the surface of the material that had changed color leaving more of the raw wood exposed. It will be a challenge to try to fix this in any easy way. 

Some things you could try:


Do nothing and see if over time the sanded areas naturally darken.
Cut out the worst boards and replace with new ones. You would have to carefully refinish those areas to get an even look.
Look at using a tinted version of the Minwax product to add some additional finish in those areas. 
Sand the whole ceiling to a consistent look and re-finish. Although this could problematic due to having applied the second coat already so sanding would have to be pretty aggressive.