Galah,
There are occasions when the ATC will be delighted to approve this, when two aircraft are obstructing each other (and could do so with the blunt instrument of procedural separation for up to 20 minutes.)
We have the ability to apply restrictions to the guy cleared VFR on top, to avoid the workload of passing multiple traffic, sep with holding patterns etc, but the idea is passing traffic in blue skies is as good as passing traffic in G. I personally will use it (at pilot request) without qualms in the case you posit.
Flight Plan Tracks are no more than a graphical representation of what we used to read off strips. We are aware that just because the green boxes have passed, the aircraft may not have. I would not base any decisions on the passing of the boxes, especially not when the decision to let somebody go VFR on top could have been made by somebody 2 sectors ago.
IFR Pick up only works before the guy has a clearance. Can't use it once he has, even if he asks for it.