The "item level is too low" warning is very misleading, and doesn't really hint at what the real problem is. As Squand mentioned, every piece of gear has a limit on how many points you can put into a given stat. As an example, the ilvl 55 crafter body piece comes with 3 CP, 92 Craftsmanship, and 31 Control naturally. Beyond that, you can meld up to 16 additional Craftsmanship, 5 additional Control, and 0 additional CP.

If you attempt to meld a materia that will take you beyond those limits, you will get the warning message, and that materia will be capped in effectiveness to stay within those limits. It really doesn't have anything to do with the item level being too low, since there's (currently) no crafter body piece with a higher item level.

If you see that message, simply use a lower grade materia instead of the one you're trying to meld. (If there is one, at least - HQ crafter feet and legs are an odd case, in that they can only hold 1 additional Craftsmanship, even though the lowest-level Craftsmanship materia still has 3 on it. There's no way to fully utilize a Craftsmanship materia on feet or legs.) There's no advantage to plugging in a high-grade materia if it's not going to be fully utilized.