What happens if the primer sequence in PCR is a mutant in the individual you're looking at? Can you get 19 out of 20 matches? What if (as I know happens) some of the exon segments flip (and thus throw off the primer matching)?
It depends how you set up the conditions for hybridization. You can set them up (stringently at higher temp) so only perfect matches stick together, or you can set them up (leniently, at lower temp) so almost perfect matches will stick together too. As to exons etc., you use a primer (usually) outside the area you want to copy, so order of exons/introns and so on doesn't matter if primer brackets the change. If it doesn't, you'll need a new primer.

How do you know you've got a unique primer? How do you know there isn't a repeat of this sequence on another chromosome, or elsewhere on the same one?
You find out by trial and error. (You hybridize your primer to cut up DNA and look for a primer that sticks only to one piece.)