I have both types, with and without chamois. I use shorts with the Sugoi Firewall tights when it is colder, in the upper 30s, lower 40s. I use the tights with chamois when the temperatures are in the upper 40s to mid 50s.

When I use shorts + tights, I prefer to use bib shorts, so I don't have two waist bands bothering me. I would say that the latter (two waist bands) is the downside of layering; on the upside, it gives you some extra warmth.