JA2:UB is a separate game for GOG. Technically speaking, they actually are separate games, even if JA2:UB was sold as an expansion, you don't need JA2 to install or run it from the original disks (nor GOG's versions, of course).
You can buy JA2 and JA2:UB or any one of the two; while in Steam you have to buy "JA2 Gold" which includes both. Even at full price for the US, GOG's JA2+JA2:UB costs the same as Steam's "JA2 Gold", and they are both discounted at GOG right now.
GOG's JA2 is Gold and comes patched to the latest official version, which is 1.12. (Source
1.13 is a fanmade mod, and as such they would need to get the permission of the creators as well as permission from the current owner/publisher of the game to include it, and then go back on it if any of the two changes their minds (like it happened on Steam, pissing people off left and right) ... waaay too much of a hassle for a distributor.
As a general rule no modifications are included with GOG games except very few exceptions, and usually only when they are absolutely needed to be able to run the games in newer systems and OSs (like alternative D3D wrappers, etc.).