OK, I've had now some time to assess the work done on my camera, and here is my conclusion on Nikken's work:
1) the (not so) bad:
- factory reset is a real pain... when you have 5 carefully tuned Usermodes it takes real time (at least 2 hours) to really get them back up. Unless maybe you've noted every step in a notebook somewhere. Some settings in the menu are usually "set and forget", and these are not so easy to find back again when you need them

But, I understand the necessity of that in their process to have homogeneity in their testing
- although the cameras was apparently nicely cleaned inside and out, there is unfortunately a new speck of dust on the matte screen. No big deal but a little disappointing. I'll try to get it out one of these days.
2) the good:
- the main reason for servicing was understood and AF was rectified within better tolerances. There is still a slight "drift to the right": my lenses now seem to need +1 to +4 but that is much better than before (all +10); at these values, even when shot without microadjustment the result is actually acceptable.
- as stated before, communication, payment, handling, and general ease of use was very good.
All in all, I would definitely recommend and use myself again their services under similar conditions. Hope this can be useful to someone hesitating some day, as I was before.
I have nothing against PM2S either, but they are less customer-friendly in the way that the whole process seems just a bit more complicated.
And there isn't any other option in France that I'm aware of!