Reason:
The names of these items are incredibly vague to the point of being essentially meaningless.
Mass Fabricator = it makes... stuff
Matter = it is... stuff
Suggestion:
Rename the two items as follows.
Mass Fabricator -> Nanoforge
Matter -> Nanites
Of course, if we want to tend away from directly ripping off Red Faction, then other names can sure work as well (do suggest).
Benefit:
Insted of saying that the Mass Fabricator makes "Matter" -- some mysterious something that does mysterious somestuff to make awesomethings -- we can say that the Nanoforge makes Nanites. These are, of course, prototypical advanced micro-scale machines that can do damn near anything. No one really knows how, it's like industrial magic. So it's still mysterious, but it's not ultra vague.