Checked the version number over on the KSP forums and its listing 1.3.1, which is also the version listed here.

If there is a file size discrepancy I'd blame compression.

Edit: I just did a little looking at the system requirements as listed here and on steam.
If what you're talking about is the listed HD space required, steam is vastly overstating how must this game needs, and I think GOG may be understating.

My install folder is clocking in at 1.9 gigs. I do have a few small mods installed. I don't know how it would hae inflated it almost a full gig unless it had to decompress some files to install the mod or something though.

Either way, that small download is apparently normal, and steam is just expecting you to install mutlple gigs worth of user made content or something.

I was going to point to specific posts but there's a few of them so I'm just going to point to the search in the update thread if you want to review them:

https://www.gog.com/forum/general/the_what_did_just_update_thread?search=kerbal

Version showing is 1.3.1.1891.

Looks like they repackaged the installers.

Hope this helps