The gleaming transmutagen specialization indicates that it gives 1 skill in Thaumaturgy per point. This is not being awarded and therefore makes it impossible to achieve rank 2 crafts in Volatile Stone, Volatile Weaving, Ominous Gloom, Ominous Call, Mercurial Blessing, or Mercurial Storms crafts.
All of the specific Transmutation nodes have the same text, aside from their name.
Each of them only give +1 skill to Transmutations using that material, and to the default Thaumaturgy ability.
The 2 crafts which use Gleaming Transmutagen do not have skill involved at all, so it would not make sense to improve your skill only when using Gleaming Transmutagen.
Further the text is slightly different. It reads: "Further your understanding of Gleaming Transmutagen and its uses. This knowledge improves your mastery of Thaumaturgy, increasing your Skill by 1 per point in this specialization.
EDITED - I was wrong on the math, it does look like you can achieve rank 2:
Skill required for Volatile Stone Rank 2 is 325.
You get 55 from Thaumaturgy, 42 from Transmutation, 30 from Volatile Materials, 63 from Alchemical Mastery, totaling 190. Add 100 from base skill and 40 from three blue tools and you are at 330, which is 5 above.
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Ah my apologies, I see what you mean.
I wonder if at some point, the transmutagen itself had quality ranks?
Edit:
It seems to odd that they’d require Concentration, since every other craft I’ve seen is simply guaranteed if you’ve got the Knowledge and the Rare equipment, along with the highest material.
Given the text differences and the fact that neither Gleaming Transmutagen craft involves skill, either (1) the text above skill should be removed from the specialization or (2) the specialization should reward the bonus skill to all Thaumaturgy crafts.
Even the bonus nodes read conspicuously different:
Gleaming Transmutagen (10): Gain +5 Skill to Thaumaturgy
Volatile Materials (15): Gain +5 Skill to Thaumaturgy and Volatile Transmutagens
The text for the Volatile Materials is also incorrect… it should be corrected to read similar to the other profs: “Gain +5 Skill to transmutations using volatile transmutagens”.
It does seem unique to Thaumaturgy to require concentration for rank 3, but this seems like potentially reasonable design to me given the infrequency that you can perform the craft.
Either way I highly regret specing so heavily into the tree. 
It is a fun little passive gold / material income. Once you have transmutagens and the ability to create mats in each of the three colors… they create more transmutagens than you use (albeit in different colors) each time you perform a craft. So once you are set up and have some points in each, you will infinitely “create” approximately 12-20 materials each day for no ongoing cost.
It is a step up from last xpac where the transmutes were all completely useless from what I remember.
I have a total of 222 skill in both the thaumaturgy recipe window (for any tier 1 ingredient) and all transmutation recipe windows (that show a skill).
By my estimation, I should be at 240 with the following loadout:
100 base skill and 18 from gear
5 points from Alchemical Mastery
55 points from Thaumaturgy
21 points from Transmutation
18 points in Gleaming Transmutagen
20 points from Mercurial Materials
3 points from Ominous Materials
(don’t judge me, I was indecisive on where to put points early on)
I only get the 222 number if I exclude either gear or points from Gleaming Transmutagen, which might be OK for Thaumaturgy, but then it would mean these skill points don’t apply to any Transmutation recipes either.
There’s definitely something not right in the skill calculation.
Don’t know why it picked a placeholder character I created years ago over the one I’m playing now.