Allright, I have done some testing and conclude how this works on my MIST, which has no RTC to speak of, using FFS 45.16 (if I recall correctly).
When I boot without startup-sequence, the date is 11-Oct-09 03:14:16, which I guess was the time I originally installed this fileystems on the Minimig. I agree that it is somewhat funny that the date is 11-10-09 followed by a clock that looks strikingly similar to pi

There is a SYS:.timestamp there, and if I do this:
assign T: RAM:
date `list sys:.timestamp lformat "%D %T" dates`
the system time is set according to what the timestamp of that file is (in my case 16-Sep-17 16:40:15).
According to above speculations, it should now simply be a matter of deleting the sys:.timestamp, and the "last date altered" of the filesystem should change. And maybe it does, who knows... I don't know of a operating system tool that can actually read the mentioned timestamps of a filesystem. What I do know, though, is that a reboot sends me back to 11-Oct-09 03:14:16.
So, it appears to me that adding and removing files to the root of the filesystem has no effect on the timestamp of the filesystem that is used to set system time on boot, or that something else goes on. Also, relabelling sys: had no effect on system time after reboot.