The Final Doom IWADs that came with the GOG versions are both the id Anthology version. The non-id-Anthology version of the IWAD pair, which is included in Steam's distribution, is more widespread. So much so that it's hosted on the servers of client-server multiplayer Doom source ports Zandronum, Odamex, and ZDaemon.

As one who owns the Steam and GOG versions of Final Doom, I kind of feel bad for players who own the GOG version alone. Because if they attempt to connect to a Zandronum, Odamex, or ZDaemon server that hosts a non-Anthology IWAD, they would be bummed. The client must match the MD5 checksum of the corresponding IWAD with the server to be able to join.

What I would like to see is the non-id-Anthology version of Final Doom in the form of an offline installer, downloadable in the Extras section.

Attached are screenshots supporting this. If you know nil about those screenshots, feel free to ask away.

Here's an iwad patcher that should allow changing whichever Final Doom versions to whichever other.

drinkybird.net/doom/omniscient