The basic distinction between the academic and traditional methods of study is that of approach. The academic starts from bottom (i.e. starts with no assumptions about the person of which he writes) and moves up. The traditional scholar starts at the top (i.e. assumes the author commentary he studies had some type of omniscient knowledge). Ideally, the two worlds should meet somewhere in the middle.
I have already discussed this issue in this post. You can see quite clearly that whereas Buckwold - the Talmud Chacham assume an omniscient knowledge on the part of the Rabad, Soloveitchik the historian comes from the opposite direction.
I think R' Kooks view is simply crucial to this question. On the one hand we need to bear in mind the greatness of the people with whom we deal - Rishonim K' Malachim - any argument they make must have merit and properly worked upon we will find the explanation. We must assume that they mastered all the relevant texts that were available to them.
On the other hand, we must also realize the limitations of the conditions they were working in.
A prime example - those who study the Taz will realize that quite often a question he asks on a Ran which after careful examination of the Ran it is clear that there is no real difficulty. The traditional scholar of today would invent a pilpul according to which there would be a heretofore unseen difficulty with the Ran and this is what the Taz comes to answer.
The Maamer Mordechai take a different approach. He simply states that the Taz only had access to the Ran as cited in the Beis Yosef and therefore he had this difficulty that to us who have the complete Ran do not find difficult. A simple and obvious explanation that in no way detracts from the greatness of the Taz.
Rashi translates Kavyustos as a kidnapper. We can unequivocally state that Rashi is wrong. The correct explanation is like Tosafos that it refers to a gambler (as the root word Kuvya attests). Does this detract from Rashi's greatness? Certainly not. Rashi's ability to learn Greek was limited to the resources he had at his disposal. But it is simply silly to say that we who have these resources should not make use of them.
(To be continued)