I've got 2 sets of "waterproof" shoes. Both are Shimano Goretex-lined.
One is the MT71 which is a shoe with a vibram sole and goretex liner. I'd class it as shower-proof, as it is a short shoe so persistent/heavy rain can get easily in the top. It coped well touring through.
The other is the MW81, an over-the-ankle winter shoe which is also got an insulated liner. Again water will eventually get in, but the neoprene stretchy ankle cover slows ingress. I've never regretted buying them as they are usefull all through the winter, even on dry (but cold) days. Hope to get my 3rd winter out of them this year.
Both shoes are much less faff than putting a cover over, and certainly much more durable (i've either ripped or worn out every bootee I've ever nought) and one of the main benefits is that there are no holes in the sole (unlike a regular shoe) as the cleat-mounting plates sit inside the sole, rather than bolting through it. So the shoes don't get water in from underneath.
My experience of sealskins results in cold, soggy feet and lots of skin rubbing.