As one passes overhead a waypoint one should;
1. Fly the aircraft as accurately as possible over the waypoint and record the time of passing on the OFP
2. Make appropriate adjustments to navigation settings and heading to follow the required track between that waypoint and the next
3. Make a position report if required.
As can be seen, item 3 will be a short period after the actual time of passing over the reporting point. If there are other stations transmitting at the time when one it first trying to make the position report, it may be longer between the time of passing over the waypoint and making the report on R/T.
In many cases, one isd making the report to a radio operator who will pass on your message to the appropriate ATC unit.
Therefore since even if you have autopilot and FMS, you will be busy noting the time on the OFP as you pass over the waypoint (and possibly also making a met observation), even in clear communications, it will usually be a few seconds or more later that you make the report.
Should you pass the waypoint at 09:05:28 = 09:05, unless you make a report and have it received in less than 2 seconds, ATC will receive the report at 09:06 or later. Do you want them recording the time as the time you passed the waypoint or the time you make an R/T report???
At a fix (and always):
Aviate - fly accurately
Navigate - record the time and establish outbound to the next fix
Communicate - make position report.