Thanks for the reply! So far, I've controlled Bionic Dues, Shattered Haven, Skyward Collapse and Tidalis. I still have to try AI War: Fleer Command, A Valley without Wind 1&2 and Starward Rogue, of the games I've bought. Excluding the logs, I've found UDA on BD and SH to be bit-to-bit identical, as well as the ones on SC and Tidalis.
The difference between the two, is the one in the games I've bought from the Humble Bundle (SC and Tidalis) seem to pack executable from all three platforms, while GOG (BD and SH) ships only the GNU/Linux updater with GNU/Linux games, which seems more logical. However, confronting the GOG updater with the folders GOG updater has in the HB updater (ArcenUpdater_Linux.x86*, ArcenUpdater_Linux_Data and UpdaterData), they are again bit-to-bit identical.
Also, that's the reason why my SC UDA was so big: included is, together with the GNU/Linux data folder, the general one, and the GNU/Linux binaries, 44.9 MiB of ArcenUpdater.app (OSX binaries and data), 10 MiB of ArcenUpdater.exe (Windows executable) and 15.6 MiB of ArcenUpdater_Data (Windows data). Removing those, together with the x86 binary I don't need, I amount to a total of 34 MiB (GNU/Linux binary is 7 MiB bigger than Windows' one).
As a final test, I ran a game I know needs some initial updates (GOG's Bionic Dues) replacing its UDA with the one found in HB's Tidalis (different game, different store). The updates completed successfully.
I feel quite confident keeping just one copy and hardlinking it in all my Arcen Games, with just a little caveat: the UpdaterData folder is probably better kept physically separated for each game, as that's the place where logs are created (ArcenDebugLog.txt and Unhandled Errors.txt) so, in case some error occurs and I need debugging, I need those files not being overwritten by another game.