Well, depending upon the level of protection you want, you should align the entire wye polarity to the turnout on the main that is thrown reverse. That means preventing one main turnout from being thrown reverse if the other main turnout is already reverse.
Controlling polarity by the wye frog alone means the wye would always be correct for one main turnout and incorrect for the other. An engine entering the wye with the wye turnout thrown against it would cause a short.
I don't think I described things very well. My apologies as I'm still recovering from a redeye turn. I don't recover from those as well as I did when I was younger.
The entirety of the wye is isolated and independent of the main. The prototype, and the model, allowed and allow, respectively, for turning passenger cars and power without fouling the main once clear. Electrically the entire wye, as well as every other non-main track, is gapped or insulated from the mains as not to trip the main line current detectors. The only electrical issue that I see is on the tail of the wye. I was thinking of power routing both rails of the tail in a fashion similar to powering the frog but not through the frog. Circuitron lists the Tortoise as been able to carry 4-5 amps through its builtin DPDT switch. With the tail being 86" I don't think the current draw would exceed the capacity.
I've attached two pics. One a screen shot showing a better look at the wye. The second an illustration literally using kindergarten materials on hand to show the polarity and gaps.
I would normally use either a DC auto reverser or a DCC auto reverser but this module will be using both at different times.