Is separation required around a 12V AC input, if its surrounded by 3.3v and logic level voltages?
voltage E field pF/cm crosstalk depends on voltage transients Z(f), which is low at line f.
current H field crosstalk depends on dI/dt current spikes and nH coupling an Zin 
layout depends on EMI immunity specs.  if you define, (using concepts above) then there is no guessing.


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supply noise, signal noise allowed ,  radiated and conducted source, level, distance
experience makes the choices easier using guard ground tracks and Common Mode Rejection (f) estimations, then test and verify when built.


In terms of lightning isolation, from line to secondary to DC, analyze your need for a line filter and MOV.  "Good" iron core transformers with 20:1 voltage ratio at line frequencies often attenuate 60dB or 10kV spike to 10V secondary from coupling factors. Ferrite is worse, due lower losses and high f coupling.