Can you wear a 100% cotton t-shirt under a FR rated shirt, if the FR shirt is rated for the appropriate catagory?

I believe so

If you consult the NFPA-70E Table 130.7(C)(11) it calls out what articles of clothing constitute each PPE level. Cotton underwear is called out. Further in the standard, in Article 130.7(C)(12)(c) it goes on to exclude meltable materials for undergarments. I hope this helps.

NFPA-70E 130.7 (C)(12) (a) Layering.
Nonmelting, flammable fiber garments shall be permitted to be used as underlayers in conjunction with FR clothing in a layered system for added protection.

If nonmelting, flammable fiber under garments are used as underlayers, the system arc rating shall be sufficient to prevent the breakopen of the innnermost FR layer at the expected arc exposure incident energy level to prevent ignition of flammable underlayers.

Also see Table 130.(C)(10) PPE & Clothing Matrix and check out HRC 2, see Notes 6 & 7.

FPN: A typical layering system might include cotton underwear, a cotton t-shirt and trouser and a FR coverall. Specific tasks may call for additional FR layers to achieve the required protection level.

The table brings up some questions for me also. For one, the table checkoff list seems to mandate layering. But the FR clothing folks I talk with tell me that the clothing is rated to a specific calorie performance Without any additional layering required. You could literally be Level 4 if you were naked under your Level 4 suit. Some of layering spelled out in the table seem extremely prohibitive to wear, just TOO many layers to even move.