On startup I do not think that any of the mods or long track patches change the Papyrus release file number which should be 22.214.171.124 which was the last update that Papyrus released and should always be used as the base gpl.exe file upon which to build all mods.
Using this patch will make GEM+ create an exe called gplc67.exe which is effectively the 1.3 patched version if you like, but, running this file will still show 126.96.36.199 on the loading screen, but, this file will work with long tracks. Running the raw gpl.exe will never work with the long track patch since GEM+ does not alter this file, it only alters copies of this file which get created for each mod.
It would have been a good idea to add the version number to the used mainback maybe. So while not ideal (you can exchange main backs) it would give a visual hint