My idea for a fix would be to not immediately consume the charges, but instead “lock” them in, allowing players to take advantage of the Inner Tranquility talent, while not being allowed to gain or lose more. Once Scrier’s Gaze ends, consume all warp charges to reduce the cooldown.
Yes, it works as intended for other active abilities. I think the issue here is that while Gaze is active, the cooldown is continually reset to the maximum, and so the Warp Charges are consumed immediately and then get overridden.