I wouldn't worry too much about the stepper sticking out the side of the gantry (I'd have called that the Y stepper but there's no hard and fast rules) as it's just basically a metal lump there's not a huge amount to go wrong as you have it. If you can't design it such that it's internal maybe consider sticking a bent aluminium box around it. I managed to squeeze my Y stepper inside the gantry (see here) but it's pretty tight and I expect to be replacing the belt more frequently that usual. That's not quite the final design that I've gone for but it shows the basic layout.