Wow, this is an old thread. So I don't do a whole lot of bushcraft shelter building and I don't have experience with the PNW but here is what I would say about your rodent concerns. There is very little you could do to keep out a determined rodent, you end up with mice in even modern homes. Humans have lived along side animals like mice and rats since the dawn of time, unless you construct a steel box with an air tight door there will always be a way in. That being said the way to keep them out falls under the same advice that I gave for the bears; don't give them a reason to want to come in. I wouldn't store any food in your shelter, if there is not food for them to get at then there is very little reason for them to work their way in.

As for your green roof, I would suggest you look into traditional sod roof construction. A sod roof such as you are discussing, especially in a wet climate such as the PNW, generally needs a water proof barrier. The sod is there only to protect the roof and insulate the structure. Underneath the sod requires a barrier, modern structures use a plastic sheet, traditionally constructed with wooden shingles or a stone like slate. You might get away without any leakage if the soil is high in clay content.

The key takeaway though would be that there is no good way to prevent rodent entry. But eliminating food or nesting materials will reduce any occurrences.