What do you mean would it fly? Will a fighter have a point deducted? Will he be fined/suspended? The answer is "It depends". It really depends on the ref and the situation.

The first situation(throwing a punch when the ref steps between fighters) should never be ok. It's hard to discipline this though, because it's hard to tell if it is an accident or intentional. The second situation, you don't stop punching until the fight is over. If a fighter is out on his feet, it's the ref's job to stop the fight.

Something similar actually happened earlier this year in the Barrera-Marquez fight. JMM was knocked down...Ref didn't rule it a knockdown, and MAB threw a punch at Marquez(who was on his knees). A point as deducted from MAB, and the knockdown was ruled a slip.