This looks like a red flag to me. Not registering the puppies is NOT going to avoid them being bred. A CONTRACT stipulating that they not be bred is how breeders do that. Since you're signing a contract, there's no reason your pup shouldn't be registered. A puppy with imperfections, if they are out of 2 registered adults, should be registered. If you get a dog that's not registered, I would be highly suspicious.The imperfections are not related to health, just something that doesn't fit into breed standards for shows and breeding so she isn't going to register them to avoid "bad breeding" in the future.
What are the imperfections?
I think it sounds fine. Herding dogs need a lot of physical and mental stimulation, but it sounds like you know that. If you and your daughter make the commitment to follow through with that, every day, I see no problem at all. You sound like a very conscientious dog owner.So, is the situation I explained bad for such a high-energy dog?
As I said, I'm concerned about her decision not to register the three "imperfect" puppies. And I would definitely educate myself on the health risks of the Aussie and ask the breeder about various testing on the breeding adults. I don't know what the Aussie's health problems are, but you should talk to someone (not the breeder) who DOES know - to find out what tests to ask about. I know there's the possibility of eye problems in the breed in addition to hip dysplasia. You don't want to take on the burden of a dog with health issues, and genetic testing of the adults is the best way to stack the odds in your favor.
Here's a place to start.
Aussie Health Tests