Hello Knightrider
I've just experienced the same problem with my SW 10" dob's focuser. I bought some astrosystems collimating tools and in the handbook it referred to the focuser alignment.
A.S. instructed to find the half circumference oppposite the focuser and spot both primary and secondary mirrors. Once I had done this I tried to line everything up and this is where it all fell out of shape.
I had to pack the focuser using folded paper to what equalled 8 pieces of paper in one corner. It was that far out. ( I used calipers, etc. for measuring). Now with that done the secondary mirror centre would not line up and was so far back it touched the spider vanes and could not be shifted to align properly.

That was at 2am and that was it. Possible causes I could think of is focuser is really bad, optics are out of sync, the tube is not a perfect circle or the system is offset somehow slightly. Either way wasn't good.
Woke up the next day and tried again using Astrobabies guides as extra help (pictures are good). I drilled a hole (1.5mm) in the centre of the focuser dust cap to set the secondary as a circle in the focuser (disregarding secondary centre point, I checked the cp twice to make sure it was right).I followed the rest of the instructions. Checked against an autocollimator and it was perfect. First time fluke i'm sure!
Like you I also went outside last night and got very good viewing. I was able to make out NGC 2298,2455 and 2432 which are about mag 10 in a suburban dark site. Don't know if that's good or not but it seems all right to me.
If it's any consolation I think being anymore precise is for the photographic department of astronomy. I'm not sure if that's what your doing though? I suppose we have to take into account that a lot of errors can be introduced into a system. Usually human error is the biggest. If you look at the price of our scopes when compared to the pro's there's a big difference so it should be same to say that the quality is also the same. I hate to say that as I love my scope and to me it was relatively expensive.
But considering that we both have enjoyed quality viewing in what seems to be flawed systems then maybe such precision isn't warranted and in the search for the perfect 'system' it is an imperfect system that is actually perfect if you get what I mean. I hear your frustration at having what seems as perfect logic fail though. I think the only way forward from here is to accept that and just enjoy the views.
Only help to give is maybe try what I did as well. Your eyes are actually quite good at judging alignment manually and I think you've come to that decision already from your last comment concerning the cheshire eyepiece.
As far as SW quality (or other mass big brand) is concerned I think for my next scope I'll build my own. At least then I'll know what's wrong with it before I use it!
Simmo