I have the same booties. Why do you need to do that? If you're wearing them in the snow in camp, then they probably won't get very wet. Otherwise, you could just use produce bags from the grocery store or something. Since the rest of the fabric isn't waterproof, unless you sealed the whole thing, I don't think sealing the bottom will do much. And if you seal the entire thing, your for sweat will wet out the down.
Maybe you can seal the bottom seams like you said and just use some good DWR on the rest of the fabric. Like Atsko Snow Seal permanent water guard or water guard extreme from amazon.