Since every other virtue and flaw occurs in parallel- -if you take warrior, you get 50xp without spending an extra year in the field, if you take Affinity you don't have to account for extra seasons in which that Affinity developed, if you take Monastic Vows or Priest you don't have to spend any time working up to it- -any new virtue is also probably in parallel, unless the virtue says otherwise. Since neither Magister nor Doctor say otherwise, I see no need for any special "sanction." But I do see a need for a special rule to say that these virtues involve consecutive years, since that would be an exception to the general case.
That said, regardless of what the rules say, what they mean, or what the authors wanted them to mean, anyone can rule however they please and enjoy.
Your way, I think Magister is a lousy virtue, skirting the edge of the List of Worst virtues. IIRC, it adds 8 years to your age and provide 240 xps. Effectively, then, the virtue is worth 120 xp (8 years already provides 120xp). That's less than 50xp/virtue point (lower than the lowest bound of any other xp-providing virtues.) Heck, even Educated is better than that. Doctor is slightly better.
The <50xp/vp aspect of your preferred ruling hints at a problem.
My way, Magister is good and Doctor is very good. Latin 5, AL 5, Phil 5... I think that's 225xp. A Doctor has 75xp remaining for Law, Medicine or Theology, not the greatest xp but still useful (Law for a Tytalus, Quaesitor or Jerbiton; Theology for the religiously inclined; Medicine for experimental philosophers (recover fatigue!) and Ex Misc with the appropriate Solomonic Art. A Magister has 15xp to be spent academically.
And I don't think a player has to go far to justify it. He put in more hours. He had some awesome teachers/texts. He didn't spend time carousing. He had some kind of magical help. He was given more seasons. His parens didn't care about using him in the lab, as long as he got the vis from his Personal Vis Source. (And my favorite, "let's just handwave, because the whole free vs nonfree seasons/year thing is just an approximation, except for lab work.")
But....