There's only three ways to identify a reagent as far as I know, either with no subtype, by a single subtype, or with a one of the modifier tokens.
1: No subtype and nothing else means you will always get obsidian unless you specially forbid it, and all new obsidian that gets made, which is cumbersome.
2: Single subtype means making reactions for every type of stone you're going to transmute, that's pretty annoying too.
3: So you're looking at a modifier token to choose your stone at the end of your reagent.
3a: [WORTHLESS_STONE_ONLY] will only pick materials that are defined as not-economic from your stocks page. This is a pretty simple way to do it and means just turning obsidian into an economic stone for the period that you're transmuting, and then back when you want to build with it.
3b: [REACTION_CLASS:TRANSMUTESTONE] will only pick materials that have been defined as [REACTION_CLASS:TRANSMUTESTONE]. This means you'll have to go through all of your stone definitions except for obsidian and add this line in there.
I don't know of any other tokens that would help in this situation. I think using reaction_class would be the most comprehensive way to do it. I'd fiddle with a new world first to make sure things work properly before trying to meddle with your existing one.
There's a crematorium mod that uses reaction classes in this way, if you found that, you could get some idea of how he uses them. Also things like gypsum and flux are handled in this way through the base game.
Haha, I didn't see Quietust's message before I posted this, so to try and be helpful instead of redundant I'll just say this:
[REAGENT:A:1:BOULDER:NO_SUBTYPE:NONE:NONE][REACTION_CLASS:TRANSMUTESTONE] as reagent
put [REACTION_CLASS:TRANSMUTESTONE] into every entry in inorganic_stone_layer except for [INORGANIC:OBSIDIAN] and any entry in inorganic_stone_mineral that you want to be transmutable. (like cobaltite or alunite for instance)