Except that most timers have an easy on/off switch. So if you have to backwash, you will have to throw the breaker for the pump. And the timer will now turn on/off the entire sub-panel at the pool unless you run a separate circuit to the pool for lighting etc.
I'm not sure I understand why it would be a problem to wire ANY wierd plug to the timer. If you can wire it to a panel/sub-panel, you can wire it to a timer, its all just wires at one end! We have a 220V, 50amp run off the main panel in the house to a sub-panel at the pool. The timer is wired directly to a 220v breaker in the sub-panel, and the pump and SWG are wired to the timer. Other circuits are wired directly to the sub-panel (pool lighting, solar controller, 110v plugs, etc).
We have an unusual pump plug as well, but the "source" side of the plug is wired to the timer.
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