Okay, I validated my suspicion. Looking at CMSync.h, they only inline the function for minimum SDKs less than 15.0. Changing our minimum SDK to 15.0 indeed fixes the problem. This is still a bug, Apple.
CaseySF
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I root caused the problem. See my post here: https://developer.apple.com/forums/thread/733383
Basically, in CMSync.h, Apple inlines the call to CMTimebaseCreateWithSourceClock (which in turn calls CMTimebaseCreateWithMasterClock) for apps that target minimum SDKs less than 15.0. This means the compiler will replace the call at compile time and thus it appears in your object code.
Your workaround is to target a minimum SDK of 15.0 or greater. I have verified our app validates at that point.