State tax filing

I'm using:  Desktop version of Deluxe on a Mac for Tax Year 2021
 
I agree with you that TurboTax is incorrectly putting Federal AGI values in the CA Form 5805, Part III table rather than CA AGI values.  As you noted, the instructions by Line 1 of the table specifically say, "Enter your California adjusted gross income (AGI) for each period".  It does not say to enter Federal AGI values.
  
In my return, TT put Federal AGI  in columns (a), (b) and (c) of  Part III, the Annualized Income Installation Method Schedule, but has my correct CA AGI in column (d).  For me, my CA AGI values are smaller than my Federal AGI values because part of my income is Social Security and CA does not tax SS.  Your situation is reversed with your CA AGI being larger than Federal AGI.
 
Apparently TurboTax did not act on your information because I saw this problem on my 2020 tax return and now again on my 2021 tax return. 
 
With the desktop version I can go to Forms and edit the values on Line 1 of the Form 5805 Part III table so that the CA AGIs will be accurate, but we should not have to catch TT's errors and fix them.  With my particular numbers it has not caused me to pay a penalty, however TT should correctly put the CA AGI numbers in the CA Form 5805, or ask us for the CA AGI numbers in the interview.