My own theory:
In a very general sense, they want to play the character that you want to earn things on. So if you are going to farm Cosmic flux for a given character, they want to encourage you to farm it on that character. This has been their overall goal behind many things, such as reputation requirements or raid kills for professions, and earning Valor to upgrade gear.
The ability to transfer is really beneficial because mains have often just ended up with so much extra, it’s a dead currency for them.
By having the tax, if you are going to go farm more, it encourages you to use that character, rather than play different ones.
Just my theory, anyway.