I think one of the reasons that Leonor is following in her father's footsteps in her military training is because Felipe believes he was well prepared for his role as King. In fact, of the current and recent Kings and Queens, Felipe seems very at peace with his education and training. When guiding Leonor, it may have simply been a situation of Felipe actively encouraging the Princess to make similar decisions. It is also not unusual for military parents to enthusiastically support their children entering the military, out of the belief that it gave them leadership and training for life outside the military.
What I don't understand, is that if Leonor did the 4 years for the military degree, would this have barred her from an undergraduate degree in law (which is what is hinted to be her future uni education)? In some countries, you can only get one undergraduate/bachelor's, and in others, you can obtain dual degrees of equal stature. Otherwise, I don't really understand why she isn't getting the full military degree, but I'm guessing there is a reason I don't know.
I think the main reason why she is not doing the full course is that she will spend one year instead in each of the 3 service academies to get acquainted with all 3 branches (Army, Navy and Air Force). The government had to create a special education program for her, which was actually approved by royal decree (the name used for executive orders in some European monarchies).