RF alignment usually refers to the alignment of the RF patch - horizontal and vertical alignment*.
the more critical would be the horizontal (left-right) alignment, as this would determine if you are focusing on exactly what you are expecting to focus on. if this is off, you would actually be focusing in front / behind the point that you are thinking you are focused on. the vertical (up-down) is less of an issue as it would not impact the RF accuracy per se, but can be a little annoying as the overlapping image is slightly higher/lower.
some (to a lesser extent) also use the term "RF alignment" to refer to the framelines, which can also sometimes be knocked off the axis.
* I may have muddled the naming convention of horizontal vs vertical alignment, but the left-right / up-down directions would give you a clearer idea of what i'm describing.