Note: I haven't yet used the Mass Fabricator, so my idea is going on what I've read on the forums and wiki.
Assumptions:
1) You use the Mass Fabricator to obtain Matter.
2) You use Matter on the workbench to craft items.
Conclusions
3) There is only one possibility for a 9-Matter recipe (filling the bench), 9 possibilities for an 8-Matter recipe (leave each of 1 spot empty), etc.
Proposal: Another form of Matter (I'm distinctly avoiding the term "Antimatter" ). Where the default generated from the Mass Fabricator would be 'Red Matter', you would also have 'Blue Matter' (for the lack of better names). The easiest interchanging would be via crafting. Red Matter --> Blue, and Blue --> Red, without anything else in the crafting window. Could make it as complicated as you wanted to interchange, but the energy to make large amount of Matter in the first place might be high enough.
Explanation: You would use Red and Blue like one would use binary in a string. So in addition to the normal recipe of (RRRRRRRRR) you would have (RRRRRRRRB), both needing 9 Matter. You would have 511 (2^9-1) possibilities for a 9-Matter recipe. Gives a lot more possibilities for higher-end recipes.
Needed now? Maybe not, but I think it might be useful later.
If I've missed something in my assumptions, let me know, but thanks for reading.