I think it's inherent to the way the digital filtering is implemented. As I recall, the 6602 manual shows a timing diagram for it.
When I first fiddled with the digital filter settings, I was also surprised (and disappointed) by the way it worked. I expected a filter output which would be phase shifted but still carry full timing resolution. Then all the valid transitions would be measured with full 80 MHz precision. Instead the filter output shows transitions that are in sync with transitions of a filter clock, which means that the effective timing resolution is reduced.
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