I think people are forgetting *how* HAM modes could and were used in productivity software, because they are thinking of style-guide compliant software ie lots of menus, lots of windows all on a high res screen.
It's a pity that the OS wasn't designed to work around HAM issues.
The left hand side of menus and windows is fine, because the border would use an indexed colour. The problem is in the right hand side where there is no guarantee how many pixels it would take before the r,g & b would get reloaded. Which is why you would often see horizontal lines across ham images when a menu was up.
If the OS extended the right hand edge of the layers by three pixels then it could add extra pixels to get the colour back to where it would be if the menu wasn't there. You could minimize the extra fringing in some circumstances, by using the closest index colour to the pixel to the right of the upper layer.
Unfortunately HAM wasn't taken seriously when the OS was designed. It was left over from when the Amiga was a games machine that output YUV, when it flipped to a computer that output RGB then it wasn't expected to be useful. It was going to be removed, but after all the years juggling to fit the functionality in agnus and denise there wasn't time/money/motivation to go through that again & then they would have spare space to add new functionality which would also have taken time.
It's pretty standard for commodore to build hardware that the software doesn't support.