1) Everything I read says the letter in question deals with conduct prior to the time when Manfred laid down the law and said future violators would face more serious penalties. (The end of the 2017 season, if I recall correctly.) So teams that were sanctioned prior to the time the Commissioner announced that penalties would be heavier received lighter penalties than those who broke the rules after his announcement? That's literally the definition of what Manfred said.
2) If the agreement the Yankees reached with the league included keeping details confidential (which is a provision lawyers routinely seek as part of settlements), then yeah, I'd expect the team to fight to protect that agreement. Trying to hang onto to the deal you negotiated with the league isn't nefarious at all.