Did some quick math, the penalty is about 10% raw stats for the i350 nq crafted so not as bad as I thought. It puts a 350 NQ chest piece actual ilvl around about 330-335ish (Other than DEF/MDEF) which is fair for catchup gear.
The NQ 350 sch book has a whopping 14 less weapon damage (-10% overall rounded up) putting it at actual ilvl around i285 for wdmg stat. Yikes that is really bad. The raw stats are fine on it though.
DEF/MDEF stats take a beating as well but not as big a deal as weapon damage.
Crafting gear seems to be about 12% raw stat penalty for NQ.
I would just lower the ilvl of the nq gear since raising the stats to same as hq (for battle gear it is already 5-10 ilvls higher than previous tome gear at HQ) would just make normal raid floors less attractive since they drop the same ilvl. Maybe fix the weapon damage if they are feeling generous.
