I just went and had a look at mine mate.It's probably a bit different as I have a 2011 FXST with the ABS wheel speed sensor on the other side,but I also have a laced front wheel, and on the side you talk about,also have a space of about 5 mm on the axle between the spacer and the fork leg.
The spacer doesn't move,so I assume without pulling it apart there is a machined step on the axle,and it's looks as though the fork leg isn't supposed to be butted up against the spacer.
The manual says to put a screwdriver or a bar through the hole in the axle to stop it from turning,then torque the nut on the opposite side first. Then it just says to tighten the fork leg cap nuts.It makes no mention of any alignment of the forks.I guess after torquing the caliper side nut first,you just let the fork leg find it's own spot on the axle,then tension the fork leg cap nuts, just making sure there is equal gap either side between the fork leg and fork leg cap.
Hope this helps.