Hi Alicia, I would hope a professor at UCD vet school would not base a prediction of allergy on a solitary study but on knowledge and experience generally.
I know that vet school very well -- grew up there actually. My understanding is that allergy treatment is actually one of their areas of international expertise? But I know opinions will differ on the issue of allergy. personally I rarely see it in dogs -- having worked in rescue for a decade and taken in a couple hundred cavaliers in my own!
No one is trying to insist your puppy has a genetic illness -- BUT as you raised a list of possible symptoms in a young puppy, where allergy would not be very common at that age, and sadly, this breed has a very high rate of health issues, it is important for every owner to at least be fully aware of these issues and have them as a consideration. You asked for suggestions about what might be going on and several people gave them. People are only trying to help you and make sure you have all the info you might need!
There aren't any differences in the genetic predisposition of cavaliers across the world so you won't see local variations between cavaliers in Canada, the US, the UK or Australia. There has been plenty of genetic work already to show this isn't the case; the breed all goes back to just a dozen dogs at the start of the 1950s, and all dogs are extremely closely related to UK stock (check with your breeder -- most Canadian dogs descend from UK imports over the past decade or two, and many use direct imports). I am actually quite familiar with a lot of the work that has been done on cavaliers in Canada because this board has helped fund many of the scans that went into grading dogs for the genetic research that is being led in Canada -- and over the years, I have been in regular contact with club members and health campaigners in Canada. (FWIW, I am also Canadian-born though I now live in Ireland -- but also know plenty of breeders in the US as well
and have a home base in California as well as Ireland).
If your breeder is responsible and fully tests (a 'registered' breeder doesn't mean much -- no more than assuming a driver with a license is therefore a great driver) -- then you should be able to very easily evaluate some likelihood of genetic illness -- if your breeder had done the basic health tests for the breed? Then you won't need to be wondering at all about the risk of DE/CC and will have a much better idea of the likelihood of risk for problems like SM (though pretty much every cavalier has CM which can cause similar symptoms).
Any responsible breeder should do the DNA test for EFS and DE/CC on both parents -- that's a no brainer for good breeders, and the tests have been available for long enough and discussed widely enough by breeders, and cost so little for them to be well aware of them -- so this will be easy to check if the breeder is indeed responsible and has done the needed testing. The breeder should also have been able to show you the results of MRI scans on both parents. Puppies from unscanned parents have a risk level approaching 75% for SM, the largest study of several generations of scanned litters has shown. These are just some obvious, easy things to check that could give you greater comfort and automatically eliminate some suggestions.
It does not cast aspersions on a puppy, an owner or a breeder to simply make sure all possibilities are being considered when trying to determine the cause of such symptoms in a pup.
Hopefully whatever is causing excessive scratching and hair thinning/hair loss will be easily determined and you will have no further problems.
But as a responsible cavalier puppy owner, it's good to have gone through all these possibilities, and you definitely will want to be fully informed about the genetic issues and always to have those as a possibility in the back of the mind if certain symptoms show up -- as vets know very little about these issues and almost all of us have found we have had to be very proactive and self-informed to get proper diagnosis when symptoms remain persistent. On average it takes nearly two years for cavaliers to get a proper diagnosis for SM, for example -- mostly from misdiagnosis of allergies and lack of knowledge in vets about cavalier genetic diseases.