I thougt that ~uptime is the time the server is up?? Why does the guides mention using this method to track bosses' time
You use it to estimate (or track) bosses' respawn time, since the majority of bosses are killed either immediately or within an hour of a server check. For example - Manon. Manon's have a respawn time of 4 to 6 hours and they are killed almost instantly when the server comes up. When using ~uptime, it'll tell you how long the server has been up or in other words how long it's been since someone has killed manon. (I.e. The server has been up for 00:04:31 - meaning that it's close to the time in which another manon will spawn, so you should spend your time camping it in hopes of finding one.) Note that as the server is up for longer periods of time, this method of tracking is skewed due to the range in time in which the bosses spawn.