if my workout focus is on time (say 45 min.), I usually exclude warm-up time and "start the workout clock" when I begin my main set. Does this seem accurate? My total time in the pool ends up being about an hour (for this example)
Warm ups should be 1/3 the distance you are going to swim during the rest of the workout. Time will depend on your ability and whether you are working on speed or distance.
Why wouldn't you count warm up time?
That's like working a 9-5 job and clocking out in the middle of the day to do work not related to your main focus (or to post on forums). It doesn't make sense. So, yes, I would count the time and distance.
That being said, remember to keep up your intensity after warm up is over, and since you are counting this time, don't swim easy during the whole workout.
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Put it like this, I do!
I can't see why you can't count all of it, warm up, cool down and the bit in the middle. Effectively you are still using energy and burning calories.