Mike, excellent point!
At first I was thinking about responding in terms of the pedagogical styles in which various particular academic institutes tend to treat the business of 'educating' their students in music theory and the crafts of composition. Some such institutes are more pedantic than others, in that they offer the student too little leeway for individual taste, style and - above all - art. After all, "education" is supposed to mean "leading out", not "shoving in", lol.
Alas though, gathering reliable info on even a few institutes in order to substantiate my contention would probably be a nigh on impossible task for the short term.
But then it occurred to me that even in private self-study, away from any and all formal institutional constraints and influences, there is still, potentially, the dimension of strict pedantry versus liberal leeway, which the student has to negotiate his way through. In my case, having studied music theory and composition on my own for about 8 years (albeit very late in life), I had to deal with, for instance, the rigidly scientific paradigm proposed by Helmholtz in his famous "Die lehre von den Tonempfindungen" (the English translation with voluminous annotation by Ellis), as well as the equally famous but far more liberal "Traité de L'Harmonie" by Rameau (Gossett's English translation). Even Fux's treatment of modal counterpoint in his classic study, "Gradus ad Parnassum", though at first sight extremely strict, offers the student at every step the opportunity - however tiny - for some art.
In these and other, more up to date cases, finding scope for my own taste, style and art was helped substantially by discovering early on that both Helmholtz and Rameau were simply wrong about the extent to which Just Intonation provides the physical basis for music; and thereafter, by developing my own appreciation of the far greater scope, beauty and versatility of Pythagorean Intonation. Also, although Hindemith's teaching of his take on "modern" composition is - pedagogically - wonderfully adept, adroit, engaging and liberal, for me it represented certain unacceptable departures from the aesthetics that I held and still hold dear. And so on and so forth for 8 long and arduous years.
So, how best is today's would-be student of composition to proceed? I think you've nailed it, Mike. Students must of course not only devise and carry out studies of their own but also practise, practise and practise with these studies, if they are to discover and develop the methodologies, shapes, forms, morphologies, etc, of their own tastes, styles and - above all - art. And all this can be ongoing, if perhaps episodic. Look how many great composers have even published the best of their "études".
In some (perhaps many) cases, this might involve waiting until after one has graduated and departed from an academic institute, given that not all of these institutes are equal in terms of the liberal scope for individual style, taste and art they afford their students. All the while, seriously ambitious students will no doubt treasure and entertain in all of their studies - institutional or private - some adroit and apposite degrees of musical rebelliousness and artful perfidiousness. But going back to my initial, cynical thought in this post, our 'advice' here presupposes that the institute does not permanently impair or even wreck the young student's chances of doing this.