In theory a lower thrust line will make the model want to pitch up a little more if everything else is the same. In reality any difference will be hidden by a very minor trim change and can be tuned by positioning your battery pack up or down to alter the 3 dimensional true CG. What the thrust line sits in line with or not isn't really an issue other than very slight effects that are only important to precision pattern flyers. Where the thrust line sits in relation to the true center of mass of the model is what counts.