The Chargers got the stadium for free in LA, whereas they would have had pay for one in San Diego. San Diego had many chances to put an offer together and refused to do so. There was a ballot issue in 2016 after the deal with the Rams was agreed to and everyone knew "this deal fails we're leaving" and they still said no. Yes they probably would have been better off had they picked another market. Maybe they could have picked Vegas and let the Raiders have LA (just to screw with the Rams) or become the San Antonio Chargers to get back at Jerry Jones for backing the Rams. Or become the Toronto Chargers, etc.
Yes their tickets are a discount to the Rams. However, they have seemed to be building a fan base. You can see now its not majority visiting teams fans anymore.
Set NFL aside because its a once a week thing and people drive long distances for an NFL game. That's why the Cardinals were fine in Glendale but the Coyotes weren't. In the cities that are big enough to support to MLB/NHL/NBA teams you have accessibility as an issue. More often than not the teams serve different parts of the metro area. Yankees drew from Manhattan, Bronx, Westchester while the Mets drew from Queens, Brooklyn, and Long Island.
As far as the Clippers go, Steve Ballmer had been part of the group trying to bring the NBA back to Seattle. When he bought the Clippers he was asked if he would move them to Seattle. He said that would be "value destructive" so clearly he saw staying in LA as more lucrative than moving to Seattle.
The problem with the "second teams" is that in each case (Nets, Mets, Jets, White Sox, Angels, Clippers, Chargers) is that the second team has almost always been poorly run. Only the Nets/Knicks are even close in terms of playing performance and that's because both of them have been a joke.