The headline is a bit misleading because I don’t think there are any banks in a similar situation to Square: a bank that receives most of their revenue from transaction processing fees and whose employees are almost all in San Francisco (San Francisco apparently apportions company revenue according to where the employees are).
Note: In California, local governments use relatively unfair gross receipts taxes instead of more efficient taxes because Proposition 13 (1978) forbids fair property taxes, and RTC 17041.5 (1963) forbids local income taxes (https://leginfo.legislature.ca.gov/faces/codes_displaySectio...). So we tax gross receipts of large companies, with 7 different rate schedules based on different industries in order to sort of approximate income.