I have major problems with this from an organizational perspective. It's true that numbers are arbitrary to an extent, but if they don't have any kind of scale then they cease being numbers and start being names; their only purpose to to differentiate patches from another, so you could call them Build Unicorn or Version Your Mother Is A Whore for all the information they convey.
But if you don't have any kind of meaningful scale in the version number, it sort of implies that you don't have any kind of meaningful scale at all; else you'd presumably put it someplace, and where better than there? That in turn suggests that you haven't really thought this through, which isn't a great position for the people in charge to be in.
So if a project consists of an eternally evolving flash game that somebody intends to continue randomly adding features to as they are suggested or come up, yeah, I could see version number being completely arbitrary, because the whole project is just Calvinball the Game Development. For anything else, not having any idea what version numbers mean and declaring them totally arbitrary is somewhat concerning.
Have you forgotten that this version of the game is called Enraged Koala?
All games in development without a clearly defined endpoint (KSP and Cataclysm:DDA come to mind, but I haven't been following a lot of games) tend to do the same thing. The version number is often just used to differentiate one release from another, and isn't in any way a countdown to the "final" version. Even some games that do have a defined "final" point use the same system where the "X" in "version 0.X" just determines the sequential number of the alpha/beta/candidate/whatever release, and once the "final" point is reached, the version spontaneously jumps to "1.0" to indicate a finalized release. Case in point, one that we're all here for - Dwarf Fortress. Yes, the version number probably still indicates the number of "core" features of the game implemented to this point, but the game will not be "complete" once 100 core features are implemented, either. Whether the game will become 1.0 or 0.100 at that point will be entirely up to Toady, and either of those will be in its own way correct.
Re: being let down by an 1.0 game: I don't suppose anybody here followed the development of Stardrive? That game was an in-development title with a release date enforced by the publisher, so the version was pushed to 1.0 as a frantic final effort was made to fix bugs with multithreading, and the game "shipped" as it was - without multiplayer, without a whole lot of features (the events and quests system was just one NPC planet with three lines of dialogue, for one), but it was still 1.0. Anyone who didn't follow the development of the game to that point and just jumped in, found a fairly interesting if buggy and in places incomplete game, that was still being actively developed.
The point about Starbound now, is that if it were in the same position and released as an "1.0" game, it would still have been acceptable. You'd never have known about progression weirdness, about the various drama, about anything but the fact that you've gotten the game you were waiting for, and while it's incomplete in places, and lacks some of the features, it's still in active development, and already quite fun to play in the meantime.