Those are great questions. Let's see if I can frame it completely and accurately. In regards to CPSR, assume that a prime contractor for T&M (through a Task Order) is awarded non-competitive contract. The prime obtains commercial T&M rates for some of the proposed rates. I believe those T&M subcontract rates are subject to FAR 52.212-4, Alternate I, requirements, even though it is commercial, the Government would have the authority to ascertain the primes compliance with subcontracting (purchasing) practices so far as the clauses stipulates.
I probably should not have used the phrase "acceptable accounting system" because that would be beyond the scope of the "Contract Terms and Conditions -- Commercial Items" clause although it does contain limited scope evaluation criteria in FAR 52-212-4, Alternate I, (a) & (i). It appears to me that commercial items are not as hands-off as intended. As you referenced FAR 44.000(, it reads that consent and advance notice requirements are not applicable for commercial items according to part 12, but part 12 requires the subcontractor to open their facilities and personnel, timekeeping, invoicing and crediting to the Government (i.e. limited scope evaluation).
My reference to "subcontractor system" refers to the billing and accounting systems.
Even if a prime is awarded a competitive T&M contract for commercial items, would the FAR 52.212-4, Alternate I, clause be past down? Does it matter?
I believe DCAA wants all commercial T&M contracts reported through incurred cost submission; thus, it falls under FAR 52.216-7? Also, recent FR suggested changes under FAR Case 2011-003; Payments Under Time-and-Materials and Labor-Hour Contracts incorporate the idea.