I really dont see your problem - there is as far as I know no need for aligning the cross table to the column. You will always use a round tool in the router and all movement of the slides at cross table would always be perpendicular to the tool. What you might need to look into is that the Z-axis should be square to the table surface of the Crosstable. The easies way to do that is to use a dial gauge on a little arm mounted in the router chuck and turn that around to see if the column is square to the base - if not you have to tram either the column or the table.
There is also one other thing that you could check - check that X-axis is square to the Y axis - normally you cant fix that on such a crosstable because there are no adjusment for that kind of errors on a manufactured unit, but you should actually rely on the manufacturer, and I do think a company like Proxxon would produce a well aligned cross table.