if the pad and the via are on the same net, then positioning the via over the pad will be seen as a completed connection, however, if you pull the via away from the pad, then a connection will be seen, so no it does not see it as routed, just joined.
Hmm, then it seems Rules Spreadsheet doesn't take that into account: nets with micro-vias that are centered on a pad are still flagged as not complete. But if I move micro-via away from the pad and then connect them with a track it's marked as complete.
As stated in Help for the Rules Spreadsheet, the Complete column is a box that is checked if the differential pair has a full track path between both pin pairs, in the case of the example, it does not.
We can recognise some inconsistency in the feedback to the user, where the net connection check reviews the status of a route differently to a Diff Pair completion as previously mentioned, the checks are different. A log 41054 has been raised suggesting that something like Auto Weld could be offered if the system recognises a nets microvia being positioned in a nets pad whilst a connection lies between them, so completing the tracking between the two.
Currently I suggest completing the track to the pad, then move the via over it.