In ideal systems the orbitals are treated as parallel because that gives the best orbital interations for bond formation. There are molecules where this is the case, where the LUMO on one molecule and the HOMO on another molecule are perfectly aligned.
The orbitals may not be parallel in all cases because of molecular geometry; but the amplitude of the orbitals may be different. The orbital amplitude may compensate for non-ideal overlap (ie, non parallel overlap). If the HOMO has a large amplitude and the LUMO is average, there is the possibility of an interaction. Here, we assume non-parallel overlap. If we increase the size of both the LUMO and HOMO amplitudes, we can get closer to a parallel overlap of orbitals. We can affect the LUMO and HOMO by adding or removing different groups (methyls, nitros etc) or using Lewis acids to increase or decrease orbital amplitude.
Also, do not make the mistake that parallel assumes perpendicular. The orbitals are geometrically aligned in space, so any intermediate that is going to form will have a chair or close to chair form intermdiate it must go through to form bonds.https://en.wikipedia.org/wiki/Ene_reaction
In this article you can see that although the orbitals are parallel they are not exactly perpendicular. (see section labelled Concerted pathway and transition states). All cases are idealised but in reality, the orbitals may not be in an ideal conformation.
I hope this helps you understand better.