I'm guessing from everything that's been reported that some mineral is quasi-randomly selected from the raws, based upon the layer type. Probably if you do get lignite or coal, you're going to lose out on an actual mineral, sort of like the wonders of cobaltite or kaolinite.
About the only way I can see to check this out (unless someone else hasn't already posted this somewhere already), is to have people start reporting what they find on shallow metal(s)/deep metal(s) embarks and cross-reference with the minerals raws. I'm also wondering what kind of results people are typically getting when it's metals instead of metal, whether it's one extra per biome change or if it's capped in some fashion.
Could even class the minerals if this is the case...
Hematite
Limonite
Magnetite
Raw Adamantine
Native Copper (because it's better than nothing)
Tetrahedrite (might not be that great by some standards, but smashy things and some armor)
Bituminous Coal
Lignite (both Lignite and Coal because if they are taking a slot for something else...well, I'd rather indulge in deforestation than lose a chance for something to smelt)
Garnierite
Native Gold
Native Silver
Galena
Sphalerite
Cassiterite
Native Platinum
Horn Silver
Native Aluminum
Calcite (it is a flux, and if it's one of two and the other was an iron bearer, I wouldn't complain)
Malachite
Cinnabar
Cobaltite
Gypsum
Talc
Jet
Puddingstone
Petrified Wood
Graphite
Brimstone
Kimberlite
Bismuthinite
Realgar
Orpiment
Stibnite
Marcasite
Sylvite
Cryolite
Periclase
Ilmenite
Rutile
Chromite
Pyrolusite
Pitchblende
Bauxite
Borax
Olivine
Hornblende
Kaolinite
Serpentine
Orthoclase
Microcline
Mica
Saltpeter
Alabaster
Selenite
Satinspar
Anhydrite
Alunite
These classes are of course, open wildly to debate, but what isn't?
I'll admit after the initial reports of the metal problems, I made my own adjustments to the raws...
[METAL_ORE:IRON:3]
[METAL_ORE:NICKEL:1]
[METAL_ORE:GOLD:2]
[METAL_ORE:SILVER:3]
[METAL_ORE:COPPER:4]
[METAL_ORE:LEAD:4]
[METAL_ORE:ZINC:4]
[METAL_ORE:TIN:4]
[METAL_ORE:PLATINUM:2]
[METAL_ORE:BISMUTH:4]
[METAL_ORE:ALUMINUM:2]
Added to every single stone. Not the greatest percentages, but that's sort of the point to me. Unfortunately, the whole map is now shallow metals/deep metals because of it.
Funny how I still haven't bothered with a metal industry on my current fortress, I'm more interested in planning out nestboxes and bee hives and trying to get another sheep, and strangely enough a cat.