AC zero Crossing detection with transformer
With a lightly-loaded transformer the phase shift will be very small, and repeatable enough to be tuned out in software.
Here's a suggestion.  If you add one more diode between the + output of the bridge and C11, you can eliminate the 2nd bridge and the optocoupler.  The bridge + output will have the full-wave rectified AC waveform.  This can drive an NPN transistor (emitter to Iso_GND) through a base resistor (re-purposed R40), and you get the same output as with the opto, but with less cost and better reliability.  Size the base resistor for a peak base current of 1 mA -ish.