While maintaining the modified date is a useful option to some (and I'd argue to those who don't care about time stamps), I think, Newbeet, you might be overstating the case a fair bit. It is rare to find software that goes to extraordinary measures to avoid affecting a file's modified date. In fact, the very semantics of a file's modified date is just that - the file has been modified. While it may seem to you that a case should be made for *minor* modifications, the change can also affect other software inadvertently (such as backup, sync or other any other software that relies on updating internal databases after a file has changed). Really what you're asking is to move the semantics of file meta-data into, and managed by, the file system. Where does one draw the line? If I change some obscure, non-content affecting meta-data in a Word document, should Microsoft Word also provide the ability to not update the .doc's modified time stamp? Or how about a Thunderbird calendar, when the only change might have been to dismiss an alarm? Or an Excel document to change one digit not affecting any calculation?
If a change is "MEANINGless", perhaps it is best not to make the change. Otherwise, you'll have to remember which files to backup too, since you can't rely on modified dates. It sounds more like your approach is to blast-copy all your files from computer to computer, rather than used change-based or time-based copies. Perhaps there is a better method.
MC doesn't have to be your central database; as MrHaugen has indicated, you can certainly write your own date tags into the files, and that way, ensure you have this data regardless of underlying file systems or operating systems.
Unless you're running an AD server, or maintain network-wide time via something like NTP, your system times are likely to be out of sync anyway. Timestamps under these conditions are gross-level at best.
So while I appreciate the request for desired behavior, keep in mind it is just one of a very long list of requests, and its implementation in general is the rare exception. There's your sand.