That's the exception, not the rule with them. I once returned a pair of wading boots that didn't measure up a couple years after I bought them -- without a receipt. No questions asked.
OP: You're buying two things -- waders and boots -- and you severely limit yourself if you try to shortcut this and get them together. If it's a money thing, consider starting with a good boot first and adding the waders later. You can wet-wade in a lot of circumstances with just a wading boot.
When you buy a wading boot, your first consideration should be the boot itself. It should offer the things you need in any good boot -- fit, comfort, support, etc. It's going to have a sole that helps with traction on rocks, allow water to move out and offer good support improving your stability in the water. And, those are all good things worth paying for. With a boot-foot wader, you'll get a slip-on boot, maybe one with some laces to tighten it up, but it's just not the same.
Lotsa good wader and boot choices already mentioned, but here's what I'm using: Simms Freestone boot and LL Bean breathable waders.
These are my second pair of Freestones. They're durable, comfortable and offer good stability. They have a felt sole. Approx $80. Maybe a little stiff though -- they're made of plastic. I might go with a Condura-type material and a studded sole next time.
Definitely go with breathable waders if you can swing it. They're so much lighter and more comfortable than rubber or neoprene. One handy feature to look for is a built-in gravel guard. It's a cuff sewn in above the ankle that covers the top of the boot and prevents gravel from coming in. Nice little feature, though you can just buy a separate cuff if your model doesn't have it.