You can have different FPC versions too.
The path to fpc is stored in the lazarus settings, so --primary-config-path allows you to do this.
If you install a Lazarus Snapshot (windows), then the fpc is installed inside the directory you chose at Lazarus-installation-time. And the FPC will have the correct fpc.cfg file.
If you download fpc from SVN, you also need to download the bin-utils (there is a separate SVN for that, or copy them from your other installation).
In this case you may have to look into you fpc.cfg by hand.