This is very true and common, and is deceiving.
The only thing I can add to the thread is that you cannot "adjust" the front sight to vertical except by rotating the barrel in the receiver, which may misalign the slide channels and cause excessive undue wear on the slide and the receiver. All features of the barrel (bottom & side flats, slide channels, gas cylinder, front sight key groove, etc.) are machined to orient precisely (about the axis of the bore) with the receiver machining when properly installed and, to the best of my knowledge, the index marks in theory mark the exact 6 o'clock positions of the barrel and the receiver units. So, in theory, when ANY barrel is screwed into ANY receiver and the index marks align, then the machining of the barrel is correctly oriented with the machining of the receiver and the slide fits and moves properly in both. I barrel my carbines by using a pair of straight bars placed on the bottom flats of the barrel and receiver and turning the barrel until the bars are parallel. I then check the index marks on the barrel and receiver and have found them in reasonable alignment in almost all cases.
The barrel should be installed in correct alignment - period, and regardless of where the front sight ends up. When the barrel has been properly installed then the rear sight should be moved left or right in the receiver to wherever it is necessary to provide the correct windage on the target. If that is way left or way right then so be it. It is what it is and that is the way it was designed to be. Personally, I have found that in probably 90% of all carbines that I have adjusted the rear sight will end up left of center in the receiver. I do not know why.
For years I have toyed with the idea of machining a series of offset front sight keys to incrementally rotate the front sight on the barrel to adjust the bullet strike 1", 2", 3" etc. left or right to POA at 100 yds, while keeping the rear sight centered on the receiver. I am not a machinist, I'm getting up in years and I don't know how much demand there might be, but it is an interesting idea and maybe a younger CNC machinist type might pick it up and run with it.
Finally, in adjusting the rear sight the ONLY rule you need to remember is that you move the rear sight in the same direction that you want to move the point of bullet impact (strike) on the target. If your shots are hitting to the right of point of aim (POA) you move the rear sight left to move the bullet strikes left. If your shots are hitting below the POA you raise the rear sight to raise the bullet strikes.
In regulating the sights, my recommendations are based upon the assumptions that the barrel is not bent excessively and that you don't want to bend ('Bubbafy') the front sight blade, which I would never do.
JMHO, ChipS