Alitum issues: Placed via/pads on PCB which is not in the schematic
You could: 
Place the vias and lock the components (by checking the 'locked' box in the properties window with the PCB inspector) so the update won't change your vias.

Or you could change the DFM rules, (which I'm not too familiar with because I'm more of a schematics designer)

As far as alignment goes, use a grid or manually force one of the graphical locations (one row of vias has all the same X values, so you could align all of the X values by selecting a row and typing in and X value). I have used excel and copied in Y values with calculated offsets. With the PCB list its as simple as copying and pasting.