When putting my last two bikes together I did that. Gives a neater cable routing at the front of the bike if you put the cable from the right shifter round the left of the headtube and vice versa. They then have to cross under the downtube so the BB cable guide routes them properly. Doesn't effect performance in any way.
My (2009) Allez came crossed-over. Inners touching, not too much of a problem, but the inner-inner (the one nearest the down-tube at the cross-over point) contacted the down-tube itself. At the very least this would have worn the paintwork so I switched them back to straight routing which then gave plenty of clearance.