I think that basically means that the last installation that runs (automatic updates runs the installation again, remember. This is not relevant to Chromium, because it does not update automatically unless you use a script, though I would not bother with an installation and just extract the ZIP instead) registers the "App Paths" for the version it installed, from what I can tell.
Since you have the canary installed, I think it will always "win", since it is automatically updated (installed) daily.
So other than somehow detecting that an installation has just happened and registering the "App Paths" back to your desired version through some automated script, I am not sure there is much you can do right now. :(