I don’t think that keeping sample data inside the song is a bad idea. Most DAWs do that, and you then can easily copy the song over.
There seems to be another reason that Renoise saves and re-encodes all samples on first import and keep it in place: So Renoise can edit the sample, non destructively. Other daws simply save WAVs.
Still I find it outdated (yes I remember you gave me a good explaination for this, what was it ) that the whole song including samples will be zipped. It should be such a hidden resource folder instead, only zipping the song xml, and keeping the samples directly accessible. It would obviously speedup renoise on song save, plus make the a lot more easy to manage the used samples from outside (maybe even adding it to Sononym etc). At least on macos such “resource” folder acts just like a file in the filesystem, and maybe Windows has such a mechanism, too?
For sake of performance while undoing sample edits, maybe even flac encoding of the samples should be dropped. It is not saving so much space anyway. Save it simply as WAV 32bit.
In the end, I think it is better, if there wasn’t added just again another option, making Renoise more complicated, but instead using a clever automatism.