Good find! The Home of the Underdogs is a great resource :).
Its noteworthy that there are different voices within the Scratchware Manifesto. Some of the claims they make ("We want to play good games, and we want making games to be an art, not an electronic sweatshop. This problem, also not unique to the gaming industry, is as old as Das Kapital and as new as The Matrix.", the critique of damages to people and environment through exploitation, and the maiming influence of market-streamlining are the major ones I did notice) are fully compatible with Underground Gaming.
The major difference is that they seem(ed) to believe that through some improvements (mainly the avoidance of publishers and big companies, who they call "vampires") the capitalist system could not only be improved but also work in their favor (see their claims about small productions that landed big hits or their citation of "Lord British" and some others), whereas Underground Gaming sees these problems as inherent to the capitalist system - it doesn't aim to create another B or C-market but to establish a parallel working society that tries to discard the basic rules of capitalism (even if only within a limited space for now, but adding to the "large picture" within our possible means by doing so). It doesn't assume that competition creates better art, even if the consolidation of power within the competition would be removed.
Seeing that the people who signed the Scratchware Manifesto were seemingly professionals working within the industry it is understandable that their aims and direction are less ideologic and more directed toward allowing them to make a practical living from their doing in the long run. This is another big difference to Underground Gaming, that is much more directed to be a hobbyist movement.
I don't want to pan them, as it is always easier to be the clever one afterwards: But imho their idea proved to not work out. "Indie"-Gaming, "Social"-Media and the Internet in general opened up channels to avoid the publishers and big conglomerates, but the structures that they criticized where mostly just replicated in a weakened form as the rules of the market still apply (you already pointed this out in the OP).
Hope all of this is comprehensible - when it comes to questions of political theory, I sometimes suffer more from my language barrier.