Universities are certainly medieval but that doesn't mean they taught scientific thinking.
There are many levels on which a topic can be understood. I was not able to take any classes in applied magic at my university, so by way of analogy let's consider music instead.
You can teach someone how to play an instrument, having them memorize a number of specific songs. If they are sufficiently skilled, they may be able to play songs by ear, and improvise songs the same way. Their ability to perform music is in no way impaired by learning only at this level.
You can teach someone musical notation, so that they can play a song they have never heard. There are actually lots of different ways to notate music. Most of the early ones only denote pitches and not rhythm. Pitches are normally in reference to the particular type of scales in use in the musical system, so they might be difficult to understand if you are used to a different one (e.g., diatonic vs pentatonic scales). Rhythm might be referenced only in relation to known phrases (e.g., Byzantine music was noted with great signs that indicated the hand gestures of the choir leaders, far less detail than modern musical notation). A musician who understands notation can create their own music (although notation is not required for this part) and also write it down for others.
You can teach someone musical theory, so they understand the differences between different scales (although probably they are still only familiar with the scales used in their musical culture), why different progressions are used, etc. This may give them an advantage in writing music or for arranging pieces for multiple instruments, although it's not required.
And you can teach someone the underlying physics, so they understand the frequency relationships of different notes, of octaves, overtones, why different combinations of notes sound harmonious or disharmonious, how and why music resonates in chambers and instruments of different sizes, etc.
I expect a lot of apprentices and even semi-spellcasters are learning at the first level. They are getting the basics down and memorizing rotes. A pure spellcaster is more likely to be learning about notation. Runes are a special form of notation that is enchanted, but if you can learn magic by studying a book there must be something that serves as a form of notation, whether it is detailed and complete or incomplete and still requires a lot of experimentation (in the analogy, the spell is written in an unfamiliar scale or the rhythm is not notated). A very advanced mage might be getting into theory, allowing them to develop their own spells.
While it is certainly possible in a given setting that the understanding of mages extends down into the actual physics of magic, it's by no means necessary.