Hi again,
It is easily to synchronize window signal with the input zero-crossing in motor control applications because PWM signals for actuation can use the same time base as PWM for window signal and thus it is known the zero-crossing event. But in your particular case, the dynamic signal is external.
Hardware workaround (offloading the CPU) which comes to my mind is the following:

You need to route your dynamic signal to two pins, one for CMP_0 and the other one for cmp1.
CMP_0 will perform Continuous mode to transform sine wave into an square wave. Then such signal is routed to LCU (though TRGMUX) to perform phase shift in order to serves as window signal of CMP_1 (again though TRGMUX). Finally CMP_1 should perform Windowed mode.
For the part in green from the diagram above you can refer to the attached example.
Such example generates a PWM signal in PTB16 (emios_0_ch_4_g) (in scope yellow signal). Receive the PWM signal in PTD15 (cmp0_in1) and replicates it in PTE3 (cmp0_out) (green signal). Then such signal is routed thought TRGMUX to PTA1 (trgmux_out0) (blue signal) and also it is routed to LCU in PTD3 (lcu0_out0) (purple signal), where PWM signal is phase shifted.
Connections required: PTB16 -> PTD15
S32DS 3.6 + RTD 5.0.0 (S32K3X4EVB-T172)

Regarding the different threshold for positive and negative transitions, it is not possible.
Hope it helps you.
Have a nice day!