Re. Paddler
I’m not going to reinvent anything I think, because whatever mechanics are at work are what they are.
I understand well enough how the sound wave forms in a flute, and around first open tonehole is the effective end of flute in 2nd octave also, where full venting is allowed below that.
To use the D2 analogy for simplicity though, the dimensionally limited working model often used

is a little cruel maybe? Clearly though, venting of the high pressure node of D encourages the formation of an octave overtone with low pressure at that point. Similar occurs with different combinations of toneholes forming partials. There is a whole load of math to figure that out and it looks impressively time consumingly official. Is that what is occuring in reality though.
You yourself say the wave is cut in half, so my reason tells me that you agree there are two waves. One inhabits the region towards the embouchure and the other towards the lower end. The waves in each are NOT the same. You would only have to take a few measurements to understand the parameters and quality of each is very different. However, they interact, they combine, one influencing the other, to fit into, in a merged way, the overiding dimension of total bore length. Harmony.
You would notice also that placing C# vent closer to where D2 would be, changes the tone and makes it purer. This is easily understandable but also underlines the point that both waves are otherwise distinct.
So picture one wave being sent out, what is happening really is that a lowered (because of lack of venting when only C# is lifted) C# note is formed in embouchure side. That wave then travels the lower portion of the flute and reflects, resonating between end of flute and C# tonehole, giving another distinct note. However when it reaches the C# tonehole on return, it encounters the next wave from embouchure side, and it and that merge under C#, they synchronise in spite of their differences, because the open tonehole is near enough both of their resonant nodes to allow/encourage that. The synchronised result matches total bore length by half, but, they are still two distinct waves, that resonate with different harmonics , but at a now common pitch, because the total reflected length (and so any isubdivision) is more decisive for that (obliges a set frequency) , than harmonic vent point.
By that model, tonehole size and placement matter, but should not be confused with bore characteristics on each side, which will also influence how or where the two waves meet. Clearly, the resonance in lower half effects how and where the wave in top half forms. Just move the toneholes and it sorts ? It would seem, but that is not what I am saying. Changing bore shape or diameter has as much effect. Same result and different approach ? Not if you are making a flute and choosing between a longer narrower bore or moving a tonehole north.