Stuff has moved around a lot over the years. I can remember when everything was in /bin, /lib and so forth with /usr being for users' home directories plus a few things like /usr/spool. Then it got more and more crowded so /u was set up for users and that started to get crowded and it was split with a /u2 before /home was used. All these changes had a rationale, sometimes clearer than others. I still don't get the rationale for putting www and mysql data in /var. Yes I know it's supposed to be for changeable stuff but you're liable to find you have to reformat it to do a reinstall because, certainly with apt based systems, there's a install-related files in there and the installer seems to expect it to be clean. I tried not reformatting as an experiment and got errors so those files live in /srv now with links back to where they're expected.