Polish uses instrumental with copulas. You can read about it here: https://en.wikipedia.org/wiki/Copula_%28linguistics%29#Slavic
Switch in negative sentences occurs only from accusative to genitive..
Yes, but it applies only to transitive verbs which connect with Accusative. "Być" is not a transitive verb and connects with nouns in Instrumental. "On nie jest chłopca" would mean "He (it) is not boy's" (He (it) doesn't belong to a/the boy) so the meaning would be completely different.
BTW, it is "dopełniacz".