Beis Medrash or SHul:Which has greater kedusha

The gemara in Megilla (27A) brings a machlokes between Rav Yochanan and Rabbi Yehoshua Ben Levi over which has more kedusha a beis keneses or a beis medrash. The nafka mina is the question they deal with over whether you can turn a shul into a beis medrash or a beis medrash into a shul. If you hold a shul has more kedusha you can only turn a beis medrash into a shul (Rav Yochanan) and similarly if you hold a beis medrash has more kedusha then you can only turn a shul into a beis medrash (RYBL).

The main question on this sugya is what is the nekudas hamachlokes. To that I have no answer.
However, there is an interesting Meshech Chochma in Parshas Titzave (29:42). There is a machlokes between Rav Yochanan and Rabbi Yehoshua Ben Levi whether HKBH spoke to Moshe from the koperes on the aron or from the mizbayach. The Meshech Chochma explains that they are l'shitaso. Rav Yochanan held tefilla is more important and therefore HKBH spoke from the mizbayach (mokom tefilla). Rabbi Yehoshua Ben Levi held torah is more important and therefore HKBH spoke from the kapores (mokom torah).