Hello benthacher,
I hope all is great with you. Thank you for using the NXP communities.
Correct. If the MCU operates at 3.3V, there may be an issue if the battery voltage drops.
You may consider the following parameters for your calculations:

Let's say that your battery voltage is 3V, it means that the PCF85063TP device will output:
VOH: about 2.4V
VOL: up to 0.6V
With such values, the communication is limited as the MCU expects VIL: up to 1V and VIH to about 2.31.
Therefore, the circuit might work, but I do see a potential issue if the battery voltage decreases to 3V or lower. It is recommended to supply both the MCU and the RTC with the same voltage level.
I hope this information helps.
Regards,
David