I don't bypass mine. In fact, I intentionally start running boiling wort through it about 15 minutes from the end of the boil to sanitize.
That said, I don't exactly follow day_trippr's procedure. I do heat sanitize, but only recirculate long enough to get the temp close on the chiller output (by adjusting one of the ball valves) I then run everything through on a single pass to the fermenter.