Which waterproof overshoes would you recommend for use with clipless pedal shoes?
For serious winter riding (I rode for 12 years all year round in Toronto, Canada, and while we had reasonable weather, it did get wet, cold, and icky a lot) I gave up on clipless, and just used platforms with a pair of hunting boots!  Canadian Tire sold -40C and -70C versions.  (I rode in -35C in the -70C pair, and I gotta say, my toes were quite comfy!) 

Tuck a pair of ski pants or waterproof pants over the tops, and that was the driest I ever attained in bad weather.

They bend surprisingly well so pedaling is not the issue, and you have good stability in bad weather.  You know, if you are sliding, and put down both feet with those big boots, you might still slide a distance, but you can control it better.

I never tried anything like you suggest, as based on other waterproof clothes, once it gets wet enough, nothing is water proof.  Everything has holes, seals, zippers, seams, etc...  They help, no argument, but not all the way.