According to table 13-6 in S12XE datasheet, there are 4 internal trigger sources for ATD modules. ETRIG0 to ETRIG3. Chapters 1.7 and 1.8 list these sources:
ETRIG0 Pulse width modulator channel 1
ETRIG1 Pulse width modulator channel 3
ETRIG2 Periodic interrupt timer hardware trigger 0
ETRIG3 Periodic interrupt timer hardware trigger 1
So it should be possible to synchronize ATD readings with PWM1 and PWM3 without external connections.