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Some people in this FlyerTalk thread seem to have done it with an appointment already scheduled elsewhere, and nobody mentioned anything about being sent away due to the existing appointment. That's about as official a source as I'm aware of.
Doesn't seem like there could be any harm in going to the Enrollment on Arrival desk at preclearence and asking. Worst case should be that they see you have an appointment and tell you to come back then. It does sound like there can sometimes be a wait, since there are limited queues that handle the process, so probably good to allow some extra time, or skip it if it's going to take too long.