It only made sense with Austin. Before Austin previous WWE champs were corporate friendly. Bret, HBK(before DX), Hogan, Savage, Backlund, etc. Austin was a rebellious redneck who didn't respect authority. It's like Iverson with the sixers in the early 2000's. Popular player but didn't like to practice and didn't respect Larry Brown. He caused a lot of issues in the front office but he brought fans to the arena, sold a lot of jerseys, and made the Sixers a playoff contender for the first time in years. He caused headaches but he made them money so they couldn’t just release him or trade him that easily.
Kayfabe wise it was the same with Austin. Ratings were up, attendance rose, ppv buyrates increased, merchandise sales were up, etc. He was a rebel but a rebel that made McMahon money. McMahon couldn't fire him because he was making him to much money but made sure his life hell.
Anything after that made no sense and it's a good reason to get rid of the corporation/the authority as the main heel in the company. It's been going on for almost 20 years now.