In re-reading your post, and also looking at the response from wheatfield, I think wheatfield is describing something different, as shimming the focusing screen is something to make the screen match the AF indicator, and you are stating these both agree.
I also got to thinking about another post
https://www.pentaxforums.com/forums/pentax-dslr-discussion/41713-focus-shifti...e-setting.html
It might be that your 50mm is a little soft at full apature and hence difficult to get the most accurate AF indicator, or MF actually right. I have not thought about this much and might be able to see how my K10D and *istD perform with my K50mm F1.4
I don't own a 28, but have had no problem with my *istD with my Tamron 24mm F 2.5 or my M42 35mm F2.
I have not tried them on my K10D but since depth of field is quite high on these lenses, what is considered in focus may not be exctly in focus.
Also, Have you considered trying to focus from infinity and also from min focus, to see if the behavior changes.
You note better performance with your longer slower lenses, which should be sharper , especially the 50mm macro at F4 vs a 50mm F1.4 wide open,, and also the 135mm which will have much tighter DOF and therefore easier to focus precicely.
Just some thoughts, before you spend forever playing with focus adjustments on the body.
p.s. I am also considering at some point to go for a split image finder, probably for my K10D when I upgrade next. I think this is probably the best solution, because just using the screen is not as accurate, and I fing the focus confirmation light too far off the field of view when concentrating on shooting.