I wouldn't mind the change, and I like how it would make finding people with crafts levelled for synergy easier. I don't see it affecting the current crafting recipes all that much--those recipes that could get easier HQ results are mostly outdated by recent gear anyways.
The change could give rise to crafting-only recipes that require double-specialization (lv 100 of two skills) that should surpass the synergy recipes (which only require that someone with the craft skills are in the party. If each double-specialization type has worthwhile recipes, then it could actually serve to decrease the number of crafters competing over these recipes, since they would have to choose which specializations to do.
Currently there are 8 craft skills (not counting fishing and synergy), but with the possibility of 2 lv 100 crafts, this would result in 28 types of double-specification (8 * 7 / 2 choices).
I do see it difficult to come up with recipes that combine certain crafts, such as cooking and anything that isn't alchemy (in before bacon mage to fix that).
An alternative to this could be to only allow one crafting skill past 80, so it would make it so that people have a 100 crafting skill and two 80 crafting skills. This could still create recipes that require a certain specialization, like 100 cloth, 80 leather, and 80 smithing vs 100 cloth, 80 smithing, and 80 goldsmithing. Actually, that type of recipe could still exist even without this alternative's limit, which could decrease competition over those recipes between crafters even further.
A second alternative would be to raise the base level to 70, and keep the 40 points--this would let you have one lv 100, one lv 80, and the rest lv 70, which wouldn't change too much about crafting.
Anyways, crafting would be pretty hectic until the sub-levels are found for the various recipes, especially since the crafting guilds don't give any hint to the level required for additional skills. That is something I would like to see--when asking for recipes at the guild, that the NPC will tell you the craft rank of the subcrafts, as the Synergy Enthusiasts do. Something like Additional skills required: Smithing (Artisan), Leathercraft (Craftsman).