Unless your intermatic timer is setup to turn on other equipment (my dual timer only kicks on the left side, not the right side which is the booster pump), it simply turns on the pump when it gets too cold, and the pump running is what protects the other stuff. That's precisely what the Intelliflo antifreeze sensor does.
My PB configured my build with an intermatic timer and I questioned it at the time saying why are you bothering with that if the pump has built in scheduling and freeze protection. He said that's just how they do all pools.. and now I believe it's because he just wasn't educated enough about how the Intelliflo works. I regret not having had him remove it from the build, because while I was having a problem with my pump a Pentair rep came out here and re-wired my intermatic to be on all the time, rendering the intermatic useless anyway. He said I should just use the Intelliflo for scheduling and antifreeze, which is what I had suspected I should be doing in the first place. Plus I imagine there is an internal battery in the Intelliflo to keep track of time and such for scheduling. If you completely remove power from the pump, I imagine the battery will eventually go dead. I'm sure it's easy enough to replace, but it makes more sense to me that it should be used as a backup, not as a primary method of retaining settings in the pump.
In any event, I have my pump scheduled to run for 6 hours at 2000 RPM and then 1000 RPM for the remaining 18 hours of the day, so it's running all the time right now. It uses such a little amount of electricity when running at 1000 RPM that it will only cost me an extra $3.00 or so on my electric bill, plus it keeps the pool nice and clean anyway.