Proof of ownership does not matter in this situation as the dog was "lawfully" released by the shelter as A) microchipping by itself is not a legally binding proof of ownership in the area and B) the dog was held as a no ID stray for the law defined 4 days (they need not be business days).
However - where things become a stickier wicket is the action beyond that. By law a person can file a petition where it doesn't matter how you got the property someone can claim that they were in fact the lawful owner and that property was wrongfully transferred. That is the crux of what we are dealing with here as the rescuer is claiming that once the dog was released by the shelter any previous ties/claims to that dog are severed which just ain't how the law works concerning property. No title / bill of sale/proof of birth and the critter/car isn't undoubtedly yours. Anyone who has taken the time to buy a car at an auction can tell you how this can bite you in the ass.
Usually how this works in most places though is that dog goes to a shelter - owner/breeder is found - rescue/shelter is happy that the dog is wanted and let's it go back to the breeder/owner. In this case the rescuer has decided that the breeder "isn't good enough" through whatever non legal decision process she has which is just silly - except when you're not expending your own funds. But I suspect in the end this will be about money - and probably a lot of it in the shakedown that will happen to get this dog back when all the paperwork is done.
If you want to make sure this doesn't happen to you:
Make sure if you microchip as your primary form of ID that you keep the info updated.
Make sure in your area tattoos,brands, and microchips are proof of ownership in your county. In many areas brands and tags are considered ownership but the rest was left out since the early 20th century.
Make sure you have a bill of sale/contract for your dog. If you're leaving a dog with someone make sure you have a clear statement of your continued claim to the dog.
If you're feeling extra nice you can always donate to the legal fund for VC (Piper's owner/breeder). Lawyers and legal paperwork is crazy expensive and this stuff adds up fast.
http://www.youcaring.com/other/bring-piper-home/223240