FTL Version questions, Humble Bundle + GOG

gog has a modified setup file (like having gog-stuff shown in the background and whatever), the game most likely is of the same version. humble may have also a modified setup, I don't know, maybe they have whatever they got from the devs unmodified, doesn't matter. But it explains the different setup version.
I'm not sure though if and how a drm free version updates itself should there ever be an patch.

probably the same thing...but the gog one could be updated automatically as new patches come out, while the humble bundle one (assuming the steam version that is) would be updated by steam (if you allow steam to) to the latest version possible, so in the end I don't think you will end up with a newer or an older version.

thanks i just wondered myself why they have other version numbers strangely...

The version numbers on GOG are for the GOG installer, not the game. The v2.xxx GOG installers use better compression (smaller download) and install faster. Most of the games on GOG have been updated to the new installer, but some still use the older version 1 installer that was pretty slow to install. That's one little thing that bugs me about GOG is that it doesn't show the game version numbers in your library (to be fair, Humble doesn't either). When GOG posts a patch, it will show on your game library something like Universal Update 2.0.3, but the 2.0.3 is just the installer version, not the game's patch version. They will, usually, later update the game's main installer to include the latest patch.