My breeder has similar views as yours does on many of your questions. When I got my first puppy from her, I was so confused because she would say one thing and my vet would say another. I have a vet that I go to for traditional things such as wellness exams and injections, but I also have a homeopathic vet that I consult for pretty much everything from flea prevention to diet to injections (feel free to PM me if you would like his contact information). My breeder makes her recommendations based on what the homeopath vet says, to I typically just consult him directly. My traditional vet somtimes - but not always - disagrees with what I want to do (for example, he disagrees with the fact that I feed my dogs raw), but I hold my ground and only have him do what I am comfortable with doing. He thinks I'm weird for having the injections in the leg, but he does it - and always asks where I "hear these things".
I waited until my dog was 9 months before he had his rabies injection (state law says 4 months) - and my homepath vet sent me some kind of herbal remedy to give him after the injection that was supposed to help prevent negative side effects/reactions. I also gave both of my puppies single parvo and single distemper injections, a few weeks apart, so it's not as hard on their system - which my vet was fine with (not all vets have these).
The younger puppy is also on parvo and distemper nosodes until about a month after he has his next parvo injection (he doesn't leave our patio right now, but I just wanted to be safe).
As for flea prevention, we don't use anything regularly, but I did spray Miles with something my breeder told me how to make (some kind of herb that fleas don't like plus water) when we went up to the woods in Wisconsin for a long weekend last fall, and he was fine - no fleas
I know it's hard to know if you're making the "right" decision when you're being told two conflicting things, but my homeopath vet made it much easier for me to make the decisions about my dogs' care. I hope this helps!