These drill dots are not needed when the pcb fab drilled your board with a NC drill machine. If you want to drill the board manually, drill dots aid positioning. In Gerber, you can use the LPD and LPC commands. Switch to LPD, plot all pads and traces, switch to LPC and plot all drill holes as small round pads with the diameter of the hole.So that positive and negative plots may be combined. I do not know how this may be done using Altium, but I am sure it is possible in a Gerber plot file.

The dot will be drilled out anyway, so it doesn't matter of the slight misalignment, and the via will have a bad connection. If you don't want a connection, you can use a non-plated through-hole, which was without any copper.