Well I admit, I'm confused here.
I took a one minute 1080 clip in a matching sequence with no cuts, no transitions and no effects, and exported to MPEG2-DVD. Under those conditions, the only place for CUDA to come into play is the scaling. Here's what I saw:
CUDA On
MRQ Off - 1:00
MRQ On - 2:35
CUDA Off
MRQ Off - 1:30
MRQ On - 4:40
We know that CUDA uses the best scaling by default. MRQ doesn't 'improve' the scaling method with CUDA turned on. And we know that with CUDA off, a lesser scaling method is used by default, and MRQ does improve the scaling. So I'd have expected to see the second and fourth times come out fairly equal, since in this export, the only thing CUDA was doing was the scaling. Yet that is not the case. It seems that MRQ is doing something, even with CUDA turned on. I believed it was forcing the scaling back onto the CPU, but the times show that some other factor is at play here.
Whatever the explanation, turning MRQ on does cause a significant slow down, with or without CUDA.