I wish you'd all stop generalising all RSPCA centres as one group. Many are totally independant, self funded, and do not put any healthy animal to sleep.
With regard to them going round to BYB... Unless there is neglect or cruelty taking place, there isn't much that can be done about it, legally! It sucks, I know, but unless they decide that all breeders must be registered, there's not a lot that can be done, apart from give them neutering vouchers, and
hope they use them.
As for the after care visit... The person who rang up will be a volunteer, who won't know or have access to the records showing vaccinations and microchip. It does sound like the person worried you unnecessarily, maybe he or she had dealt with a not so nice person, and was a bit worked up?
The visit is basically to see that you and the kittens are happy. Also you can ask any questions you may have. The volunteer visiting you
does not have the power to remove the kittens, he or she will just report any problems back to the centre, who will then investigate further if needed.