That's possible as it was made for the Retail/Steam version. You might send a PM to 0X90 and ask him what he thinks.
GOG uses it's own versioning that rarely if ever matches the dev's version numbers. You should look for the dev's version number for the if you can. Check for log files or look on the gog forums or elsewhere.
Example: I have patch 1.54 for xenonauts from gog for the game. GOG lists the patch as patch_xenonauts_220.127.116.11 however the game lists itself as being patch 1.54.
[Edited by Varacka, 6/11/2015 10:55:56 AM]