I have the same issue, when I update my "1- BASE PRICE" it does not update the rates in my calendar. Maybe it only changes the rates for new availability when they come online? If so it should say that somewhere.
The problem with using the "2 - CUSTOM PRICE" option is that if you want to set the new rate for large periods of time it won't let you do this if there is a booking already within that time frame. Changing rates for seasons, etc should be able to be done easily and independant of whether or not there are already bookings for those days. Most property management systems out their allow you to set different rates for as many time frames as you want, up to 1 or 2 years ahead of time, and this is very helpful to set different prices for seasons, weekends etc.
Airbnb needs to end the BASE and CUSTOM Price options and go with a simple Rate Page, where you input a rate, select the date range it is valid for, and select which days of the week it is valid. This is the standard with property management systems and should be a no-brainer. Then allow manual rate changes for specific days on the calendar to make on the fly adjustments for last minute discounting, holidays etc.