Bossanova;
The Project, as described, is going to require several different Derating Methods, as the Wiring Methods will be a combination of Two different Raceways:
EMT and Metallic Wireways (AKA "Gutters").
Suggest reviewing Article 376 prior to any choice of installation.
With the Wireways, there are Two things for consideration, per Section 376.22 - Number of Conductors and Ampacity:
376.22(A): Cross Sectional Fill.
This limits the Wireway to a Maximum 20% Conductor fill.
Equipment Grounding Conductors _ARE_ included.
Although there may be 541 #12 THHN CU. in a 6"x6" Gutter, without exceeding 20% fill, the next part kills that idea instantly...
376.22(B): Adjustment Factors.
Where the Total Current Carrying Conductors does not exceed 30, no Derating is required.
Equipment Grounding Conductors _ARE NOT_ counted.
Having 31 or more CCC's will require Derating Factors, per Table 310.15(B)(2)(a), as follows:
a. 31 to 40 Conductors: Adjustment Factor = 40% (Imax x 0.4),
b. >40 Conductors: Adjustment Factor = 35% (Imax x 0.35).
As you can see, there is a point where either (A) or (B) will influence the Wireways.
Along with the Wireway issues, feeding them with Raceways, such as EMT, has an altogether new Conductor Fill and Derating concept to figure in.
Using Section 310.15(B)(2)(a), exception #3, if the Segment of EMT between the Panelboard and the Wireway, does not exceed 24", the Conductors may be installed without Derating Factors applied, so there is a little give-way in that situation.
Good luck!
--Scott (EE)