Yeah, it's unlikely that many users would wear just the hooded shorty alone. However, Waterproof does mention that option in their product description, "This front zip vest is designed to blend and compliment our W1 and W2 5 and 7mm wetsuits or to be used as a separate shorty in warmer waters."
I suppose the recommended method would be to take your wetsuit and and hood in when you visit a Waterproof dealer with many sizes of the Hooded Shorty in stock and see what fits. Since I don't have a Waterproof dealer nearby, I thought I could ask and get an idea of what the likely fit would be. What I have done is take my chest, waist, hip measurements while wearing my 7 mm W1 fullsuit. It moves me up a size for the shorty. If the fit is tight for the given measurements, which it seems to be on the W1 (at least, on me), then maybe go up two sizes on the shorty. That could leave enough room under the shorty hood to fit something more substantial than the cap...maybe a full sized hood with bib, resulting in a more water tight fit. It might be a 3/5 hood rather than a 5/7 hood, but combined with the shorty hood, it should be plenty.
I would be interested in hearing from anyone with a hooded shorty...how does it fit compared to the W1? It doesn't seem like they have the sizes listed to fit over some other suit (ie. if you wear a medium W1 7 mm, get a medium size shorty) because they suggest it can be used alone, with a 5 mm or a 7 mm suit...or I suppose whatever else you are wearing. So, wear what you want underneath and then get the correct size shorty to fit over that.
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Looking at the size chart on the waterproof.se website, rather than the waterproof-usa website, head sizes are listed for the hooded vests. They are much more uniform than for separate hoods...and somewhat larger. So, head size should not be a primary concern regarding fit. The hood on a hooded shorty is likely to be big for your head unless you either have a big head for your body size or you wear a separate hood underneath it. If you size the hooded shorty to fit over your wetsuit...the hood will be loose unless you do wear a separate hood underneath.
Yeah...if you want a good fit...go to a dealer with your size in stock. That said, at least I now know the hooded shorty one size up from my W1 has the same size hood as the shorty 2 sizes up from my W1. So, the only question left...how tight a fit is one size vs two sizes up from my W1?