(final response for the archives)
While MCEBuddy encoded the show for loading to the Zune, it took a very long time (>1hr) to convert the ATSC file and also >1hr to load to the zune. (hence my request to avoid a double encode).
In addition it didn't look very good. The source (HD soap opera) was 4:3 aspect ration and the image was centered on a wide-screen display. MCE Buddy didn't know to crop those out, so the whole thing was shurnk making the video portion tiny.
The best solution I found was to use "Free Zune Video Converter 1.0" from http://www.dhost.info/jack1024/zune_converter_en/
It's basically a front-end to the common FFMPEG command line tool.
It took 4 steps
1. rename *.ms_dvr file to *.avi so The zune converter knows it can read it (ffmpeg doesn't care)
2. convert 1920 x 1080 source video to 428x240
3. Crop 54 pixels from the left + right sides, leaving a 320x240 video
4. Load to zune.
Step 2 took about 1 hour for 1 hour of HD, but steps 3 and 4 were pretty fast because the file size was small.
The end result was an excellent quality video on the Zune.
Robert