I'll answer my own question from back then.
I tried to look at the issue (wether iMovie does a re-encode or why the label of the file is DV before edit an passthrough export and then DVCpro50 after the passthrough) with someone in the doom9.org forum and he looked at the same frame from both before and after and said they are bit-identical. In other word, are the same. He assumed that since the application was written with NTSC in mind Apple might have done something wrong with the labels for PAL, after passthrough, so an App like mediainfo (or others) would report a different codec (DV vs DVCpro50). If that is the reason... who knows.
But I am a bit more satisfied now, to know, that it is bit-identical - that is, if it says that both files are the same.
In the meantime I am still searching for a better "work"-codec for S-VHS captures. I mean the codec the editing/capturing software uses,
- while saving the analog material digitally to disk
- I am working with the file (editing, cutting)
TERRATEC Video-Rescue e.g. allows YUV422, AIC, DV, DVCpro, DVCpro50, mpeg4, H.264. mpeg4 and H.264 are obviously not suitable.
I understand that AIC would be better than DV (guessing from the chart here 3.3MB/S versus more https://en.wikipedia.org/wiki/Apple_Intermediate_Codec#Format_Details
What about YUV422? What other codec not tied to using iMovie10+/FCP or Pro-Software (Adobe, Edius,..) would be better? I understand ProRes would be the best of all but overkill for VHS, right?
The wiki article about AIC says
Both MPEG-2 HDV, AVCHD and the Apple Intermediate Codec record a 4:2:0 component (Y´CBCR) digital video signal. Each sample (pixel) has a resolution of 8 bit. This is not much of a concern for editors as HDV and AVCHD records in a 4:2:0 color space anyway. In fact you may actually lose data if you decide to use 4:2:2 codecs like DVCPRO HD
It is quiet interesting that more can look worse.