Is this expected? I guess it could be because the PWM signals are from the same timer.
Yes it is expected, you guessed right.
Do you think it is possible to get PWM signals out of phase from the same timer,
No it is not.
However you could get the timer to generate an interrupt. Then the interrupt service routing will toggle the pins in a quadrature fashion. You will need four interrupts for one quadrature cycle.
Alternatively you could always use microseconds delay.