http://forum.square-enix.com/ffxiv/t...948#post308948
3. Materia Craft and HQ
When turning weapons/armor into materia, it will not matter if the weapon/armor is HQ or not. Similarly, when adding materia to weapons/armor, it will not matter whether the weapon/armor is HQ or not. (NQ items will be useful when mass producing materia.)
That was from a Yoshi post a few days ago.
Herp-derp...point was you could do all of those things in gear you wouldn't normally be using. You can keep those points flying way over your head while you're at it.
This really depends on how long it takes to actually convert an item to materia. If it doesn't take that long it won't matter much.