We each carry a clear plastic trash bag big enough for our pack to fit inside. It is always the first thing on top inside the backpack. Pull it out first and either lay your stuff on it as you unpack, or shove stuff in it to keep it dry. My tent is always at the bottom so everything generally has to come out to get to it. Being clear means I can see where my other sock or warm hat has gone off to inside the bag. Hey, the price is right and it works.
boots and clothing go into your pack to keep them dry. put the pack under a small tarp and store it outside your bivy bag. if you don't have a tarp just position your pack so that the armloops are underneath the pack so the part that touches you stays dry overnight.
cooking is also done outside the bivy bag. just cower under the hood flap in inclimate weather and stick your arms out to do the cooking.
Fly Creek UL1 making coffee in the morning. No headroom to sit up, but plenty of width even with a 20" wide sleeping pad. Old tarp at the door for taking boots off, but it could easily be rigged as some sort of vestibule extension. I just hung my pack on a small tree outside for the night.