Well, when it came to the original gear, alchemist, culinarian, and weaver were on items like robes that gave large boosts to magic craftmanship, and blacksmith, goldsmith, armorer, and alchemist were on doublets that gave large boosts to craftmanship. However... I think that whether it's physical or magical is based on the recipe itself. Some disciplines may have more of one than the other, but I don't think any discipline is exclusively one or the other. I've even heard some hypothesis that recipes require certain amounts of both, and what's considered a "magical" recipe is simply a recipe that needs more magic craftmanship than it needs regular craftmanship.

Of course, this is all hearsay and conjecture. I don't know for absolute certain how the system works, and I try to just keep a more or less even amount of both.