Syag, actually it is questionable if they have a halachic right to be flexible as it is not their airline.
Lit,
1. See Why do airlines make a big deal out of single-piece baggage weight limits? on quora.com. See my previous post for the rates of different airlines, some of which are even higher.
2. So be late in NY and early in Israel.
3. I would like to hear their stories of rude customers who scream and yell about another &200-$300 on a trip for which they are paying thousands, especially when it’s their fault. I have been on both sides of the bureaucratic desk so I can tell you that there are always two sides. Maybe you should read one of the “dan b’kaf zechut” books.