I am using the macOS version of TurboTax and went again through the entire California questionnaire, but did not find an MCTR box to check there. Maybe, this is different for the online or the Windows version. Actually, there should not be such a box in the California questionnaire if there is already one in the 1099-MISC questionnaire. This is certainly not user-friendly and may lead to inconsistencies. TurboTax should be smart enough to automatically correctly reflect, in the California tax return, the existence of CA MCTR based on the radio button for the 1099-MISC.
The requirement of having to delete the 1099-MISC and reestablishing it again rather than just turning on the appropriate button looks a little bit like random programming.
Btw, I tried something else. I tried to introduce the CA MTCR as a subtraction under "Other Adjustments to Income" in the California questionnaire, but it did not show up as a subtraction on Schedule CA(540). It still remained an addition on Schedule CA(540).
