-- Last Updated: Sep-30-12 5:41 PM EST --
Chota makes a version of their boot with the Goretex top, where the top goes well up the leg, like traditional hip boots. They can also be rolled down in some way to a more standard height, like a little below the knee. This style of boot was new this spring or last - I have forgotten which. Unless it didn't sell well, I'd expect it to still be available.
I often wear rain pants over standard-height Chota boots. As long as I'm reasonably careful about water depth when I step out of the boat, that works fine. I can see why a taller boot would be nice at times though.
As far as safety goes, water getting into extra-tall boots when swimming shouldn't be much of a problem, because even though they will have plenty of water in them, that water weighs nothing until you climb out, so as long as they don't balloon-out to full volume and become cumbersome (which doesn't happen on boots with a cinch-strap top) swimming isn't hard. Modern Gore-tex waders are amazingly safe and easy to swim in for the very same reason (the "danger" associated with waders refers to the traditional kind, which are made from 15 to 25 pounds of rubber and rubber-faced canvas and have quite a bit of a "funnel top" even when using a waist belt). But once you climb out onto shore you'll still have a good bit of extra weight "on board".