nozzle size shouldn't effect layer height.
Just wall thickness.

Think about it, you'll still be able to extrude a 0.05 layer, it'll just be wider.

No logical reason for nozzle diameter to effect layer height.

Also with version 3.0 of s3d. I don't think you need to have two seperate processes (or earlier versions come to that) Each nozzle has it's own seperate settings anyway.

Essentially a dual print profile is already two seperate processes combined.

Probably easier to do it with 2 processes though if you want vastly different infill from each nozzle.