Um, Besweet can use Aften for AC3 encoding. AC3Enc is also available.
SoundTouch is strictly used for changing pitch, tempo and rate. It can be used with any output format AFAIK.
When recoding AC3 to AC3 I always decode and make any changes as uncompressed PCM.
When I'm ready to encode back to AC3 I use SoftEncode. It has been out of print for awhile, but it's still commercial grade DD encoding compared to someone's sourceforge project.