The majority of stereotactic imaging units combined with a LINAC use two sets of KV beams which are placed 90 degrees apart for getting a stereotactic image. If the angle between the KV beam source is around 100 degrees, will it make any change?
It depends on the implementation of the solution. If you have a set of fiducials markers with more than 6 markers for each projection, there is mathematical solution for non-orthogonal projections. On the attached publication there is a presentation of the method.
Any way, the short answer is YES. You can use 100 degrees between projections, but the math is harder, that is the reason for some systems to be fixed in 90 degrees.
Chapter Imaging, Stereotactic Space and Targeting in Functional Neurosurgery
The advantage of using orthogonal verification is the isolation of the vectors of motion to adjust for matching the initial position; the frame-of-reference adjustment vectors for matching become more complicated if an orthogonal evaluation is not used. Use of non-orthogonal angles can certainly be done and ExacTrac system from BrainLabs uses a 60 degree separation, not 90 degrees:
http://www.google.com/patents/US8396270
Modern computerization permits quick separation of the x, y and z vector adjustments, along with pitch, yaw and roll.
Perhaps the main reason to prefer orthogonal images is that physicians are more used to deal with them (to recognize the anatomy and to registrate DRR and KV images). And of course, you don't need math expressions to convert it into couch displacements.