I think you have touched on a fundamental problem that all whistle makers face, and flute makers even more so. There is not just variability in the way different people blow. There is also variability in the way the same person blows from one day to the next. Also, temperature and humidity change from one day to the next, and these directly affect the tuning of a whistle or flute, even if the player’s blowing remains constant.
For a maker this is an impossible problem to solve when tuning whistles using a tuner or RTTA. By definition, if the whistles you make are precisely in tune, according to your tuner, on the day they leave your workshop, and if the blowing style is held exactly constant, then your whistles will be different to each other, simply by virtue of the fact that the temperature and humidity change from one day to the next. Similarly, if your blowing technique varies from one day to the next, and you tune your whistles based on your tuner, then your whistles will embody the variation in your own blowing technique (ie., they will not be the same as each other).
I’ve struggled with this problem myself and come to the conclusion that what you need is a reference flute/whistle for every particular model you make. I always keep hold of the best instrument I’ve made to date so that I can use it as the reference. If you have yet to make a good instrument, then buy the best instrument you can get your hands on from another maker, and use that as the reference. Then when you are fine tuning your own instruments, on any given day, you simply manipulate their tuning until it matches that of the reference instrument.
If you do this, then you will get consistent tuning and response that matches that of the reference instrument. If you chose a good reference instrument that is liked by good players, then the tuning of your own instruments will also be liked. You simply can not achieve this by using a tuner or RTTA.
If you chose a bad reference instrument, then the tuning behavior of your instruments will likely not be enjoyed by players who are used to a different pattern of tuning and response.
Ultimately, I think, for a maker, consistency is more important than tuning. Without consistency, you can’t have consistently good tuning.