As suggested above, DVDA Studio 3.0 definitely allows one to bring in AC3 audio if it is multiplexed with the video, at least in an Mpeg 2 (.mpg) file. I have done it numerous times.
In particular, after encoding a camcorder DV avi into audio .wav and video .mpg files, I convert the .wav file into an AC3 (.ac3) audio file and then multiplex the .ac3 file with the respective video .mpg file. This results in a multiplexed .mpg file with both the video and AC3 audio. DVDA Studio 3.0 accepts the multiplexed .mpg file with no problem.
I do it for the obvious reason -- to preserve more room for the video, allowing higher video bitrates, that will still fit on a single layer DVD.