Well, you may be perhaps an edge case, but most people have much higher limits on their credit card than money in their checking. I’ve probably got an extra zero.
Your contract with them probably gives them the right to do this.
I don’t know what to tell you, these are the reasons. They don’t just want to pay an extra 2.5% processing.
As a general rule, you can assume if all the players in a large and competitive field do the same thing, and it doesn’t make sense to you, and the alternative you think is better is both obvious and easy to implement, then it’s because they know something you don’t. I assure you, major car rental cos know everything they need to about the difference between debit and credit cards.