Lee, this is quite common on Notrun Commando's. Many years ago, a friend & I did a parts survey with 10+ cylinder heads. Gordy and I both used to work for a Aerospace casting company and he theorized there was significant core shift on many of the castings. Surveying cylinder heads you could see the evolution of many.
Dies and molds are expensive, Gordy is a Tool & Die maker so he is an authority on this topic.
We found significant differences in the heads in the exhaust ports alone and accounted for major differences in how the pipes fit as well as aligned. I only have 3 cast iron heads and 4 alloy ones for BSA Preunit twins and not enough to have a scientific comparison but I spent some time "eye balling" mine and believe there is variations in the ally ones, the cast iron ones look more consistent but I cant be sure at this point.
(To test, mark and measure a precision surface plate, then install a very LONG piece of tubing in each one at a time using a fixed mount, longer the better. We used a surveyors/construction laser to measure with,)
Point is, I suspect the reason SOME people have no issue and others do is that there is a disparity in castings, followed by engine mounts, frames, brackets etc. As they say in construction, You may be off only an 1/8th of an inch here, but at the end you will be off by 2 ft. (Accumulative)
I have some railroad construction tools (6 to 8 foot long) steel bars of various styles and made some sleeves for various OD & ID and use them in a fixture for gentle persuasion, and a torch in others.
As to your construction debacle, talk to some contractors. One of my former co-workers had a portfolio of properties and had the same issue in one small town. Had a bit of a dispute with the officials. But in his opinion any barriers you place in front of him are merely obstacles to navigate. In his case the rules always have a loophole. He found like you, they wouldnt approve a new structure but no one can restrict maintenance of the existing one. (Well they can, but its hard to limit the scope).
So what he did was rebuilt his one small section at a time and over a period of time. In his case it was limited to so many square feet so he rebuilt section by section just under that sizing. When a major feature had to be left in place he either built over it, or behind it. Code compliance spent months monitoring him but over time he rebuilt the entire house. I bet your locals know of some tricks and ways to beat the system.