It seems that get_iplayer repacks the MPEG-TS files into MP4 ones using FFmpeg, adding quite a lot of garbage data.
When I losslessly repack the resulting MP4 files using mp4box instead, these files end up some 5 % leaner, and I even added the 1200/675 pixel image into the metadata.

So what are you asking? If you just want a larger thumbnail, configure that with get_iplayer.

EDIT: And what are you classifying as "garbage"? If it were garbage, don't you think you would notice problems during playback?

I have noticed that 1/2 hour programmes have grown by about 30mb since 2.99 from just over 160mb ish to around 190mb ish

It's obvious that a lot of useless garbage data is added in the process of converting the downloaded .ts to an .mp4.
The amount varies but I noticed files with data crap in excess of 100 MB!
This useless data can be cleanly removed by repackaging the .mp4 using the freeware mp4box - I do this all the time since I don't need the embedded metadata but put my own in there :
mp4box -raw 1 movie.mp4
mp4box -raw 2 movie.mp4
mp4box -add movie_track1.h264:fps=25 -add movie_track2.aac -new movie_repack.mp4
The data garbage and cleaning operation do not change the embedded video and audio data in any way, so you only gain storage space - which adds up after a while.
The author of the scripts should scrutinize the way the final file is assembled using ffmpeg, because I think this is the culprit.

A little homework goes a long way. Do yourself a favour and actually examine the files. For whatever reason, ffmpeg produces much larger sample tables and other internal structures. Nothing wrong with that, and not "garbage". Nothing I could  do in get_iplayer to change it, either.

This is completely irrelevant to get_iplayer. Thread closed.