I'm using the GOG-version of BG3 too, but meenwhile using their Launcher "GOG Galaxy" (because of similiar update-issues during last years esp. with CP2077). When i start GOG-Galaxy-Version of BG3, LariLauncher shows the correct Version '4.1.1.3648072', no issues with my savegames so far (still at the End of ACT II).
Is this old-version-Issue only related to GOG-offline-installed Variants of BG3?