The basic premise is that mods mainly use non-canon ships included in the VP files that come with it and campaigns mainly make use of canon ships in the original FS2 VP files, or otherwise use ships from other VP files that do not come with it.
Examples of mods are Blue Planet, Inferno, and the FreeSpace Port, as most of the ships used in their centrepiece campaign do not come from any of the original FS2 VPs or rely on VP files from another mod or campaign.
Examples of campaigns are Warzone, Derelict and Destiny of Peace. The former two use ships from the FS2 VP files, while the latter uses ships from the FreeSpace Port.