Some answers
1. Changing timelength inevitably requires re-encoding. I don't know of a native linux encoder that comes close to Aften for quality but as you know it alone won't do the timeshift. I would imagine ffmpeg would allow you to demux to wav whilst altering the framerate. You could then feed the wav file into Aften.
2. The ac3enc.dll shipped with the last release of BeSweet is nowhere close to Aften in terms of quality but it's all about what you're happy with.
3. You could try putting Kurtnoise's updated bsn.dll file in your BeSweet directory, along with a Windows compile of Aften.
http://kurtnoise.free.fr/BeLight/bsn_20070513.zip
http://aften.softpedia.com/
then navigate to your besweet directory and use a commandline along the lines of
wine ./besweet.exe -core\( -input Extracted_audio_1.ac3 -output Encoded_audio_1.ac3 -logfile C:\temp\Encoded_audio_1.log \) -azid\( -g max \) -ota\( -r 25000 24000 \) -bsn\( -exe aften.exe -b 384 -6chnew -readtoeof 1 \)
(note -6chnew only necessary for 5.1 streams - omit this for stereo)
Alternatively, search for "eac3to wine" - see if you come up with anything useful.