Start with why you feel I need to fix my calibration algorithm and why you feel that using the ideal model does not explain what I am showing.
I think that you wrongly assume that the same rules apply to both rectangular waveguide- and e.g. coaxial line calibrations, which is a honest mistake.
In the SMA coax calibration world, it's perfectly normal to ignore the parasitics of your cal standards and use "ideal" coefficients, as you correctly stated. An SMA cal standard, having let's say 1mm of transmission line before the actual termination (50 ohm resistor, open, or short) means an insignificant phase shift at let's say in the sub 5GHz world.
If your center frequency (I'll refer to it as 'f' from now on) is at 2GHz, the added phase shift at 2f caused by the parasitic 1mm transmission line will increase, but will still be negligible.
In the waveguide world however, (as I said above) the only way you can present an infinite impedance (equivalent to and "open" standard in the SMA world) is by transforming a short, with a 1/4 wave impedance transformer, which you achieve with a 1/4 wave offset short.
The phase shift of a 1/4 wave transmission line around f is not just a parasitic - it's predictable, and is extremely abrupt, so much so, that at 2f, your 1/4 wave offset short standard will look like a short again.
And I think here's where you wrongly assume that phase delays around f in a 1/4 wave offset short are just parasitics, and therefore can be ignored.
The phase delay of a section of transmission line that has a length that is 1/4 wave is extremely significant, and by calibrating it out (i.e. assuming it's just parasitics) you essentially take the ability away from your VNA to measure phase meaningfully.
The calibration algorithm for waveguides therefore have to compensate for the phase shifts when using an offset short.
I hope this helps, an I can assure you that your articles were interesting and useful, I just wanted to point out a concern (independent from your articles) with your method of calibration which is worth looking into.