Can you play 99 relentless rats in commander?
Yes, you can, for the same reason you can in other formats.

The first Golden Rule:


  101.1. Whenever a card’s text directly contradicts these rules, the card takes precedence. The card overrides only the rule that applies to that specific situation. The only exception is that a player can concede the game at any time (see rule 104.3a).


They'd have to ban or restrict the card to limit its use, but it's legal in that format.