Why is the QuantiFast denaturation step different for PCR and RT-PCR runs in the two-step protocol for the ABI 7500 and other cyclers?

This is due to differences in composition between PCR and RT-PCR buffers. QuantiFast PCR Buffers are optimized for fast amplification with shortest possible PCR steps, while QuantiFast RT-PCR Buffers are optimized for reverse transcription and subsequent amplification.