I would hope that they controlled for such systematic effects in the experiment (did not read the paper) by mixing individuals from both groups (my guess would be that they do not look different). I guess they should have also modified some other random gene in the control. Did they actually?

However, I find it very interesting that all those important details seem somewhere hidden in the paper. Also I guess if you consider a 10x increase between the species and then end up with 4% this sound really far less spectacular.