WinSCP synchronization does not compare file contents. How could it do that? Most FTP/SFTP servers do not support calculating file checksums. Without that, comparing file contents could be done by downloading complete contents only. Then, the synchronization would have no advantage over mere complete directory download.
Having that said WinSCP is newly (since 6.0) able to make use of shell (if you have a shell access to the server) to calculate file checksums. Eventually, we plan to make use of that functionality for synchronization. You can vote for it here:
Bug 52 – Use file hash as criterion for synchronization
Also, I do not understand why you blame WinSCP for incorrect timezone of your server. Have the server fixed.