Point well taken. An "inexperienced" person could even come close by putting a mark on the cork where the mouthpiece ends, and then remove the mouthpiece and measure the distance from the end of the neck to the mark on the cork. When I attempted to recreate Benade's and Gebler's method of finding the "equivalent volume" on my alto mouthpiece, one of the steps was to first measure the "geometric volume" and then calculate the volume of the cylinder displaced by the insertion of the neck. Subtracting that figure gives the actual "geometric volume" used. For anyone interested in the method used I have attached a pdf of my procedure.
I put a mark on my neck cork (or my mouthpiece does it for me) where it plays in tune. The only thing that affects whether I place the mouthpiece on that mark or away from it is my calculation of how the lead trumpet player's current divorce proceedings are going to affect his pitch. That's more complicated than the missing cone calculation.
With regard to the OP's question, while all these discussions on missing cones and chamber sizes are correct they don't completely answer it. One other factor to consider (strongly) is embouchure pressure and position. Additionally there is t the effect of the player's physical makeup - your throat and mouth interact dynamically with the mouthpiece and reed, so what "in tune" looks like can be markedly different for different people.
The missing cone concept DOES come in to play with the procedure I use - I try to adjust the mouthpiece so that my horn is in tune with itself. I do this by matching the pitch between B2 (LH index finger alone) and B1 (low B) overblown. I "slur" between these fingerings until the two pitches are in tune. Then I try to play in tune with the mouthpiece there. Theoretically this is the point where the "missing cone" is replaced by effective mouthpiece volume.
In practice, this meant (for me) that I had to relax my embouchure, the side benefit being that my tone was better. It may not result that way for everyone, but usually people that have tried this approach end up pushing in a bit.