I would like to use an MD5 checksum as the mode of comparison when using Tools->Synchronize. MD5 is an option for Tools->Find Duplicate Files, but not for Synchronize? For my use case this means the only reliable comparison option is byte comparison, which I expect is slower than an MD5 checksum. But since MD5 is an option for duplicate finder, why is it not also an option for Synchronize?
I would say the opposite since reading every byte will be necessary to calculate MD5. You even add the MD5 calculation algorithm to actually compute the MD5.
Byte comparison might be complete after reading just one byte from each file 
MD5 could be faster if the checksums are cached.
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