I pretty much always use all of my bivi's with a thermarest or kit mat inside and this tends to stop the material wrapping around the legs. In the summer my standard set up is a "top bag" made by rab (basically a down bag with fill in the top and nothing underneath, just pertex) to save weight and bulk I often team it up with a 3/4 thermarest and when doing this put my overnighter pack down the bottom under my feet to prevent cold spots. In the winter I have chucked my boots in a plastic bag down in the bottom as on one trip where I'd left them out side they froze with the toes curled up and took an age to get comfy in the morning (I initially tried them wrapped and placed in the head end as a pillow - it's not as bad as it sounds but they can pick up some pretty earthy smells from the ground your walking on, it's not the smell of my feet, honest

). If you try this then a plastic rubble sack is ideal, it prevents additional water dampening everything else, and are really useful to sit on in damp ground conditions (cost pence and weigh next to nothing as well).
I did do a small adaption to one of my bivi's that may work for you, but it needs something to drop a line over. Basically sew a small loop to a goretex repair patch (probably any repair type patch would do but I had a black round goretex one floating about anyway) and then stick it (self adhesive) over the seam at the top of your foot box (half patch on top of bivi, half on sole area), this placed the small loop at the top of my foot box and meant some 3-4mm Bungy cord could be thrown over a branch in woodland (other end weighted with a log/stick/stone allows some movement without stressing the join if you wriggle or you have to peg the bivi down), or you could thread through a walking pole loop before pegging to the ground on moorland. This works really well if your using the hoop and pegging the bivi down (bit like a two hoop bivi) but does add to the phaff factor and sometimes you either don't have walking poles/paddles/branches or just want to keep it simple

.
The Saturn model with the twin hoops has a mesh vent at the foot end to improve airflow so I'm afraid in the Jupiter on multi day trips turning everything inside out and airing over a line or the canoe every now and again is the only way to go.
I hope all my blathering has helped a bit rather than muddy the waters further, any other questions just ask
