Nice to see that my post finally resulted in a larger discussion. Let me take this as a chance to report a bit on my progress.
I have to agree with Ventura that this is painstaking work. I finally managed to restore and tune the treble side, but it took me many weekends and the Christmas break to arrive there. Of course, I was particularly slow as this was the first time I did everything and I also had to repeat some of the steps, e.g. waxing and tuning, several times until I arrived at OK results.
Following debra's advice, I did not try to pretune the reeds before waxing them back to the blocks. I don’t think this would have made much sense as the accordion's condition was quite bad in the beginning (some reeds were stuck, leathers falling off etc.), so that I could not record valid cent deviations in the beginning.
After waxing and replacing the leathers, I then went for the approach where I calculated cent deviation twice, i.e. once with the reed block inside and once with the reed block outside of the accordion. What was really helpful for this, was a kind of sophisticated excel sheet that I set up, which allowed me to calculate the target cent deviations that I have to achieve outside, so that the inside deviations become zeros. Also a tuning software, which allowed me to first record all the frequencies and then simply copy-paste them into excel was really helpful.
I have attached some example plots that I have done in excel which show how much inside tuning differed from outside tuning.

Nevertheless, even with this approach, I learned that I have to do another fine tuning, with the reeds back in the accordion so that I can get all the reeds deviation within +/- 1 cent. With time, I lost my fear of this approach and learned that it is not so hard to tune reeds while in the accordion. Especially after I learned how to use the reed hook properly. The accordion is only a 32 bass and not so heavy, so I could test each reed individually on the accordion's bellows, lift the treble, turn it and tune the reed easily, but I can imagine that this becomes more difficult with a more heavy full size accordion. Also as it is an old box, I didn’t have to worry much about putting some scratches to the grill or similar damage while having it turned around and doing the tuning. As I do not have a dedicated tuning beelow for this kind of tuning, I was simply using the accordions below. I would be interested in the others' experience, whether you can do some damage to the bellow’s frame if you repeat this step too often?
One thing that was particularly annoying with this accordion, was that there are no individual registers for all the reeds, it only has a M, MM, and LMM switch. So while tuning the L for instance, I had to block off the other reeds. This was particularly difficult when I then tried to get the octave clean between L and M, where I constantly had to block the M on and off.
Nevertheless, in the end I arrived at a result, which sounds OK to me and I have now more confidence of doing some tuning on my more expensive accordions. At the moment I am still working on waxing and tuning the bass side of this accordion. Overall with the limited time I have it might take me almost half a year to get this job completely done. That's OK for me, as I did it out of interest and fun, but it also showed me what is the value of this work when done by a professional.