I think most bike shoe booties won't fit over a midweight hiking shoe because of the differences in what the sole thickness/cushioning system in most hiking shoes. I haven't ever tried it, but i think you are out of luck there. I think that's what you are asking, Waterproof hiking shoes versus a hiking shoe with a bike shoe cover?
my advice? don't worry about it, keep your feet dry rotating 3 pairs of wool socks in whatever footwear you've got. Waterresistant as possible. If you have cycling shoes, by all means get booties, but neoprene toesies might be enough and would be nice to have along as well.
and why, why isn't there just one cycling shoe with a simple goretex bootie? I don't want neoprene lake moon boots, rather something like the winter jogging shoes you see on the market by montrail and solomon.