You evidently have a lot more experience with tuning than I do, as I have only myself to experiment on. However, I have tuned a lot of bows to shoot 3 under, as I enjoy buying and selling bows and shooting different bows.
I have never had a problem tuning a modern recurve to shoot carbon or aluminum arrows. However, I also like to enter longbow competitions where wooden arrows are required. I have found it difficult to tune wooden arrows to shoot in the lighter weight longbows I would like to use in competition. It seems that within any reasonable range of what I want to shoot, they indicate weak. I could go to a really heavy arrow, but that would defeat the purpose of what I want to do. So I just trust the feathers to straighten them out and they shoot pretty well.
I assume with your experience, you know to start tuning with the nock point set too high and the shaft purposely weak to avoid false positives, so I won't dwell on that. But I do believe there are certain bow/arrow combinations that resist 3 under tuning, apart from whatever problems the archer may introduce into the process.