Oh, I am quite willing to accept that it is not the fault of SFTP or Winscp. As alluded to, maybe the cause is backup/restore (across a DST change) or zip/unzip (across a DST change). Also, when occasionally I'm on the same LAN as one of these servers, I'll use Samba and TotalCommander or xcopy/d/s for sync'ing (and this is an additional source of ambiguity in the time stamp, I think?).
The point is, this sh** happens (to other people as well, I hear) and it would be sooo nice if Winscp (even though not at fault) would help us out.
Maybe you don't like to clutter the nice program with all sorts of options?
But consider this: There is already a 2 sec. tolerance built in when Winscp compares time stamps. The 1st request simply amounts to making that tolerance a variable. (Maybe to some other user, a 2 sec. slack it too much...)
Though it would be good to be able to additionally specify a tolerance of 'modulo a few hours'.
Of course, a related request is that for rsync support
that would allow to efficiently compare files by content