The assembly instructions show the first type of Blum locking devices that were used back when those instructions were originally written and put together. We use Blum Movento slides now, so the slide type, and therefore the locking device type, has changed multiple times over the years, but the general installation process remains the same.
Today, we use two types of locking devices: the older Tandem version and the newer Movento version. Moventos are standard on Barker Modern projects, so the locking device you are showing is the correct one for your drawer box.
As for the holes, these are hand-drilled by a human on site using the locking device as a guide. We drill three holes so both types of locking devices can use the same hole pattern. If the holes are slightly off on one side, then the jig may have slipped or something may have shifted during drilling.
Easy fix is to simply hold the locking device in place and drill a very small pilot hole, about 1/16″ deep, at a 45 degree angle. Then attach it using the screws provided. Pretty simple.
Photos attached showing the locking devices and the hole placement used for each type.