I think in reality you can only master a specialization and should only happen by basically practicing that specialization repetatively. At least, that's how it is in RL, not sure if it translates to fun gamplay. Historically, the blacksmiths who made knives didn't make swords, swordsmiths didn't make armor, armorsmiths didn't make tools, toolmakers didn't make decorative ironwork, etc...
A game needs to be fun to play so too much of that kind of specialization can ruin it. I would say that crafters who reach "max level" can specialize and only through specialization can they gain mastery. One way to accomplish that is to have certain alloys or rare items that benefit from mastery. Think "wootz steel" for swordsmiths. For alchemists, maybe a rare plant that is normally poisonous but when processed perfectly has benefits. Start with high failure rate and reduce that failure rate as the material is mastered.
Of course you could do material mastery without specialization. The specialization would happen naturally as certain materials would only be good for certain types of crafting (weapons vs armor), and the work and repetition to master a material would make it not worthwhile to master multiple materials. Then build progression off of that.
Material based mastery also draws a lot of parrallels in the real world. I watch a blacksmith on Youtube that is primarily a tool maker and works with different steels. Another youtuber sent him some wrought iron (the real stuff), and he struggled with toolmaking using it. Even though he is a master smith, the material properties were different enough that while he understood the differences and how it has to be worked differently, he didn't have the practical experience which hindered him.