Ability timers increasing when overused

This is not entirely true.

Revali's Gale has a 6 minute cooldown, which can be reduced to 2 minutes after completing EX Champion Revali's Song (Champion's Ballad DLC). However, it can be used 3 times before it needs to cool down.

Just like Revali's Gale, Urbosa's Fury and Daruk's Protection can be used 3 times before they need to cool down. The only ability that is different, is Mipha's Grace, which needs to cool down after each use.

The cooldown timer always stays the same unless you do Medoh again for the Champion's Balett DLC. But you will have to use it three times before the cool down for it starts.

The ability timers, as per this answer, are:

• Revali's Gale. 6 minutes after all 3 uses
• Mipha's Grace. 24 minutes after 1 use
• Daruk's Protection. 18 minutes afer all 3 uses
• Urbosa' Fury. 12 minutes after all 3 uses

These cooldowns can only be changed by two methods, both of which speed them up by a factor of 3:

1. Completing the Ex Champion Ballad Trial. For each ability, this occurs when you beat their associated boss as part of the Ex Champion Ballad Trial, for example Thunderblight Ganon for Urbosa' Fury. An in-game message will occur after you beat the boss telling you that the ability will recharge faster. This is permanent.
2. When inside a Divine Beast or Hyrule Castle. This only occurs when inside these areas, and stops when you leave these areas.