if you are using a windshirt like its "meant" to be used … size it snug enough that you wont be flapping in the wind like a flag
especially with active pursuits … the snugger it is the better its "breathability" (theres a reason why gore requires its active shell to be snug) … and the less it gets in the way
usually just large enough so that it can take a fleece or UL down jacket under …
when at quick stops simply put the puffy over the windshirt … sure you lose a bit of "warmth" vs putting it under … but you arent going to be faffing around taking your windshirt off, putting on the down jacket, then putting back on the windshirt when its only a short time … youll lose more warmth with that process, not preserving the built up body heat … and in windy conditions, a recipe for losing a layer
in camp you can put the light puffy under the the windshirt … or if its a larger puffy, put it OVER … for rain as someone has mentioned it makes more sense to size the RAIN JACKET to fit over everything, rather than the windshirt, and simply put that on
;)