In the long run, it's a wash no matter how you use them. 10% is 10%, whether that's today, tomorrow, or 6 months down the road.
Two trains of logic on this one, based on one's personal preferences and risk tolerances:
1) The save for an uber TM logic (conservative route): 10,000 runs is an awful long time, and the TM in question is too powerful to fuse duplicates to speed up the process. Moogles are applied specifically to this special TM either in a giant batch to max it out quick, or as moogles are obtained to focus on this special TM (like dual wield).
2) The time-value-of-money [TVM] logic (aggressive route): Moogles don't become vintage with time and gain additional value by sitting in inventory for a rainy day. As 10% to a given TM is the same 10% applied to any other TM toward obtaining that TM, logic would dictate that moogles should be applied towards current in-progress TMs to accelerate their completion as the benefits of a completed TM now far outweigh the benefits of completing that TM later (ie: you can clear something with that TM now that you can't clear without it).
I used to be in the first camp, but have migrated into the second camp over time. That said, I will tend to allocate moogles to TMs that I only have one unit for to speed them up in lieu of having a dupe to sacrifice, as 10,000 runs is far, far longer than 4,750 runs fusing two units together for that same TM.