Once you know each speaker's zenith, azimuth angles, plus their distance, you know their positions in 3D space relative to the main listener position. It boggles the mind why they would do this and not apply it during rendering, that would be fraudulent. They say they do this in their own manual, so if it's a lie, then that's actionable.
Of course, I haven't seen independent verification at how good their Atmos rendering truly is, compared to a baseline with only speaker distances relative to fixed speaker layouts, but that shouldn't be too hard to test scientifically. It's just that AVR reviewers don't have the will nor the means to.
Ambisonic rendering has been done with knowing speaker positions (measured by hand or by triangulation) since the 70s when they would put 8 speakers at the corners of a square room and pan sounds around in 3D with a joystick. Without knowing the actual XYZ distances between speakers in a home theater the 3D sound cannot be accurately rendered. And before anyone chimes in, XYZ <-> Zenith, Azimuth, Distance is just a change of basis, i.e. 100% equivalent mathematically.
Here's a description of YPAO 3D from a review
"For the Atmos channels, Atlantic Technology was kind enough to provide two pairs of the 44-DA Atmos-enabled speaker modules (review coming soon) to complete a 5.1.4 Atmos configuration. Since Atmos capability was not enabled out of the box, I downloaded the new firmware to get it. Next, I set up my speakers using Yamaha's proprietary YPAO. The version of YPAO included with the RX-A3040 uniquely includes 3D and Angle measurement, which is not an advancement to be taken lightly
. Our Yamaha rep describes these options like this: "The Angle measurement is used to correct for speaker placement that deviates from the commonly used ITU-r placement. Furniture, windows and room layout can prevent many people from placing speakers in the proper location. By knowing where all speakers are placed in relation to the prime listening spot, the DSP processing can image the signal to more closely match ITU suggestions. Meanwhile, the Height Angle measurement is used
, among other things, to give the Atmos decoder more accurate data on how to map the individual sound objects within the listening room
. If the receiver knows that the front right overhead speaker is 45 degrees to the front instead of 60 degrees, the decoder can more accurately place the sound of a mosquito, for instance, in the three-dimensional confines of the room."