Hi Courtney, I don't think the angles are that pronounced that it would impact the weapons. If you were to strap a 9L (seems so last century) slightly off boresight the angle would have to be compensated for which, as you know, is pretty easy to do in almost all of its modes.
Of course, I think a pure boresight mode of aiming your missile is pretty low down the list of options. Radar, IRST, EO pod, helmet cuing, Link, DAS etc for HOBS with digital IR seekers is all the rage. (Although I think most still miss the more intuitive analogue sidewinder growl when compared to the synthetic imitation in ASRAAM).