There's a few variables that can add to poor shifting such as wear on components and even a dry chain.
Maybe try going a bit beyond settings suggested by Park tool.
I've found that if I follow it to the ť I will have poor shifting to the smallest and largest sprocket so I back out the limit screws a touch and all is better.
Also having a rear suspension I find that what is perfect in the stand doesn't always translate to perfect on the road and I need to tweak a hair.
That said I've had it running perfectly for months and then drop the wheel and have it off by a hair myself... So I know what you are talking about. Doesn't happen every time... But enough that I am aware of it.
Barrel adjustment on the shifter is my friend.
Until we got our ebikes with front and rear through axles I just assumed it was mostly marketing hype; more stable, better control, etc, etc. For once, it's not hype. At this point in my life I am hard to impress, but these axles did it. No hype, just better...