I believe with fuel injection, the atomization is to enhance the evaporation of the fuel. You don't actually 'inhale' the atomised droplets, cos they going to hit your valve or another piece of cast ally/steel somewhere. That's also why you enrich your mix during cold starts, there is not enough heat in the castings to evaporate all your fuel yet.
I woudn't be to worried about the injection angle/direction, your tune will definitly be able to correct for the differences. (You tune cold-start conditions differently depending on 'wall wetting' parameters.