Rarely is a three way timer switch (if such an animal exists) useful. But a regular timer switch can override a 3 way switch setup to do one of: hold the light on all the time or keep the light off all the time.
When the timer is overriding the 3 way switches, you cannot easily set the 3 way switches so the light does what you want when the timer stops overriding, except if you remember which 3 way swithc positions do what.
(One morning on WRKO Radio) The tub's not clean! Let's remodel the bathroom.
(One afternoon on WRKO Radio) It's time for an oil change. I'm going to trade in the car for next year's model.