The "upside" of the fee is nothing more than feeding the voracious appetite of the state of California. The explanation for this AMT franchise tax literally uses the phrase "for the privilege of doing business in California". The state tax board knows what it's doing, and it doesn't care, because the truth is that loads of people want to start a business in California or run a business from within California as a resident, and have no other choice but to pay the AMT franchise tax (even if the business is incorporated in Nevada or Delaware, if most of the business occurs in the state of California, the tax man still cometh).
It is greed. Plain and simple.