I just got that app and sampled it with the two bikes that are here at our vacation house. Looks pretty cool and simple to use. It was able to detect slight differences in tension. It has suggestions to get more accurate results. And over versus under shouldn't matter, because it says to use the length (and diameter) or the spoke only from bottom of nipple to the first crossing, which makes sense from an engineering perspective.

I'm not planning to use it to build wheels from scratch (been doing that by feel, ear, and no tension meter for more than 20 years with great results). But I see no reason it wouldn't work just fine.