Merry Christmas
These are great questions and I am glad you are doing your research early. My suggestion would be to have your little one microchipped at the same time you are neutering him. I know articles say it is not painful but one of my dogs was done at the pound and believe me it is a large needle and he did yelp. It is not the end of the world for pain but since you have to neuter your dog then I would do it while he is under. Your vet will already have microchips so I would see what kind they have but I am going to assume they have the Home Again. My gang of 10 are all microchipped with the Home Again program and one with Avid and it is a national one time signup program. My dogs can be scanned at any vet, humane society or pound as long as they have the Avid scanner. As you know Banfield has been blocked from selling their micro-chips but the following article is interesting and will give you an update on what is going on.
http://www.canismajor.com/dog/microchp.html
Even if this is passed it will take a long time until all dogs would be on one microchip and if I understand the article correctly it will only be a suggestion, not a requirement. I would be more concerned even if you went with the new recommendation that shelters and vets would not have the newer version so you would still have a problem as the majority of dogs would have the older system.
I think you will need to ask what kind of scanner does your shelter have and what kind Petco is using along with your vet. This is not the time to save $$$ if only a few places can scan your dog and this is why Banfield got in trouble as many people assumed their dogs could be scanned anywhere.
I know my shelter has 2 different scanners and I have taken one of my dogs to make sure he can be scanned at the shelter and the humane society as a test for the gang. I also have my vet check each time I have taken a dog in to check for their chip to make sure it can be read. In very limited times some chips have moved but this is limited. It is just part of my yearly wellness check with my vet...no big deal.