Ichan,
There is another post in this forum where an owner was frustrated with issues related to alignment drift and accuracy.
This maching is designed [as are all PnP machines] to access a clean reference marker on a board, or panel border - fiducial.
There are two problems with using a hole [although it is also round] :
1.
It is 3 dimensional, which means the light source will likely have a substantial effect on the 'shape' it sees once the gamma is set high - eg no grey tone, just black and white.
At best you will end up with an ellipse - certainly not a circle. What is 'seen; through the hole will likely also have some effect on the outcome. Would highly recommend that you place fids on all boards, and also on panel boarders, especially if there is no space available on the PCB.
I believe once that issue was recognised, the placement drift and accuracy issue disappeared.
2.
Although the through holes are usually very reliably placed, each PCB house works to different tolerances.
This means that the actual through hole 'could' be offset from the footprints by the amount in the 'tolerance'.
What this means for component placement is that you are now placing in reference to a location that is 'not known' relative to your footprints.
I recommend you place fiducials on all future runs of your boards if you are going to use a PnP machine.
Your contract manufacturer most certainly would have done so in the past, if only on the panel borders which may have been removed prior to delivery.
This board has no fiducial so i will try to use drilled holes, also i want to try the bad board detection on the coming machine.