You could do it either way, really. I was looking at having the effects categorically separated for a couple of reasons. First, it would make it easier to tweek the ratio of effects that happened. Generic effects would be things that did not directly affect gameplay or had only extremely limited affects on gameplay, where as others might affect future combat or magic. This way, you could shut off the magic effects, without shutting off the combat affects, and without having to tweek each and every entry. There is actually no reason not to do both. That way, you could set rates for the category and for the individual effects within the category.
That completely breaks the entire basis upon which the reaction webs idea is built upon.
That would be a matter of implementation. Ideally, it would be tag based so that it could be structured and set up in the raw files. For example, Magic could be disallowed on common quality items, but allowed on Mastercrafted and Artifact, similar to the way entities are able to allow/disallow reactions/jobs/workshops/etc.
That is not what this system is trying to achieve.
"Magic" properties are just properties. The game does not judge whether they are magic or not, in the same way that nether caps are just another type of wood that happens to be ice cold at all times. All items made of nether cap wood are going to have those "magic" properties, and item quality has no bearing, nor could it have bearing, because a nether cap wood log has no quality, and has that same property.
Likewise, the properties come from the inherent nature of the materials themselves - to achieve the latent potential of the materials requires the alchemical mixture of materials that react with one another, not some sort of making sure that the seams of the wood are kept unnoticeable or exquisite decoration.
A tile is one space of the map, a 1x1x1 area of the world. I thought that was pretty much standard lingo for the number of times I have seen it used, even by you. Although, I am not certain what you are referring to a 'list of tiles'. The lists I have been talking about are the lists of properties/effects for your alchemy set up, and the tiles are space in the game.
... that is severely confusing. What do tiles have to do with reactions?
Are you saying you want different hemitite walls to have different properties? If so, you're radically misinterpreting the concept. The properties define what material I am talking about.
There is no randomness there - property tokens A, B, and C have to be there for it to be called hemitite. If it is hemitite, it means there are property tokens A, B, and C in it. The name "hemitite" is just a label for a material consisting of property A, B, and C. If it doesn't have those property tokens, or has more property tokens besides those, it isn't hemitite at all.
Likewise, reactions are what take place inside of workshops, so tiles should not come into this at all.
Because of statements like: "That is to say, the point is to free the system up from the confines of strict raw control over what can be achieved, and invert it into simply having raws be the things that set up limits on what can be achieved."
This sounds like you are attempting to make more of the process hardcoded than perhaps needs to be.
You're totally misunderstanding that, then.
I'm saying that instead of having raws where you have to iterate out each and every reaction that a dwarf is capable of performing in the raws, what you would do is simply set up a system where every reaction is possible unless you specifically deny it to them through use of the reaction webs.
That doesn't mean it's hard-coded, that means everything is raw-modded, but that the way that you enable or deny things from happening in the raws is changed.