First of all, do you only want the 3.2 install? Or do you also want the 3.0.4
The installer offers a 2ndary install checkbox, and if checked will ask for a separate dir for the conf, which you could set to an empty folder (even inside the install).
For all else, it knows where your fpc used to be. You can change this either in the setup dialog (if it is showing during startup), or under Tools > Options.
I am not sure why it did not upgrade the version itself.
Also there is a 2.0.6 - 3.2-beta download, but it might have the same issue.
As far as the link goes, not sure why this shows on Windows. It applies to Linux only where fpc is a separate download.
For windows you can download fpc standalone from the fpc site. The Lazarus installers for windows always bundle it into one installer IDE+fpc.