The pip upgrade upgrades the code base, not the station data. The configuration file, weewx.conf, is part of the latter.
To upgrade the station data, you use "weectl station upgrade". By default, this upgrades the documentation, examples, and utility files, but it can also (optionally) upgrade the configuration file and skins. Because we work hard at backwards compatibility, that should be necessary only rarely.
It's best to think of the version number in weewx.conf (and, for that matter, the skin.conf's) as "Installed by", not the current version.
If you want the current version, use
weectl --version
You're not the first to get confused by this. I'm thinking at the very least to put a comment in weewx.conf stating that the version number is the "Installed by" number. Or, even removing it completely.
-tk