I'm glad I could help!
In Linux (or any OS), if the patch update button is not appearing in the game, then that means it was not able to talk to Amazon S3. The two likely causes are "check for updates" being explicitly off in he settings for the game; or a firewall or other OS permissions blocking the game from contacting internet servers. That connection for an update check is the only network connection it makes.
Incidentally, the separate updater executable is actually more of an unpacker. The game itself does the update checking and downloading, and then fires up the updater, which just unpacks everything and restarts the game. Since we didn't get to that point, it's definitely a network permissions issue. I had thought it was having trouble after starting the update process.
Glad the manual patch workaround worked, though!