The max_md5_file_size only affects the behaviour of the MD5 column if you have it displayed in the file display. It lets you stop enormous files having their checksums calculated automatically.
The Synchronize tool does not have an MD5 mode; it only has a straight byte comparison option, which compares the full file byte-by-byte. There would be no real advantage to an MD5 option as the whole file has to be read anyway in order to calculate the checksum.
The option for MD5 accuracy you mention is only applicable to the Duplicate finder tool.