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Au contraire.... I agree with everything.
In principle it is a better way to measure tension, but in practice I suspect any app will be largely inaccurate due to the above reasons (length of the free spoke, gauge, taper etc...). The beauty of the three point bending method is that it is relatively simple to use, it can be calibrated for accuracy, it is very reproducible and the tool is robust and compatible with workshop use.At Easton they use acoustic probes to measure tensions and generally their wheels are well tensioned. They are still crap though, mainly due to terrible hub/spoke interface design
It's not without its own problems, but it has the potential to be cheaper for a given level of accuracy and precision than the more common load/deflection method because frequency measurement electronics are much cheaper than load cells. The problems are 1. You need to have a good model of the spoke to translate resonant frequency into absolute tension and 2. spokes which touch at the crossing might not be resonating at the fundamental frequency of their full length, they are effectively stopped (think guitar fret) at the crossing, or they might be vibrating like something which has another spoke attached to it at the crossing point. Acoustic tuning therefore works best in a factory where you're building a lot of the same design of wheel; you build the prototype using a very expensive load cell, then measure the dominant resonance of the spokes on that wheel and issue the tuning to each building station for replication using cheap frequency analysers.
For home builders, acoustic tuning can probably get your relative tensions more closely matched than a cheap tension meter (and will certainly be faster), if you have even a modest ear for harmony, but you'll probably still want the tension meter for absolute tension.
I'm sure @ugosantalucia has had his say on the issue before, and may wish to take issue with me again :-)