Design 1 is definitely better than 2 because it's more space efficient & will cost less to build. If you want FR water after the skimmer compartment, simply place your FR pump in compartment 3 while leaving the FR in compartment 1 would do. Anyway, I don't see much difference since some of the water will definitely flow into compartment 3 without going thru' skimmer.
My current sump is similar to yours. I found out that the 2nd drain pipe into refugium contributes to much detritus in my refugium & compartment 3. (I could put a sponge between 2 & 3 to keep 3 cleaner, but that would restrict pods from getting into main display.) So, a regular cleanup of compartment 2 is a hassle that I regretted. Worse still, the dirt affects the performance of my return pump over time. From hindsight, I would have done better by having only one drain pipe in compartment 1. Allow water from 1(partially skimmed) flow to 2, then from 2 flow to 3. My chaeto would probably grow as well, & the pods would have a great party in there too.
Just my thoughts.