No, it is not correct. Here the preposition "en" contributes to the construction called "gérondif" ; it is the equivalent of a subordinate clause (ref.). The subject is "Averroès"; the grammatical fonction is "indication of manner".

You could translate as follows.

• Averroès used the method of "commentaire littéral", following Aristotle’s text, dividing it and explaining word by word the various parts, to extract finally the meaning.

The last "en", as you noticed, is not rendered by the same form; "en" does not presuppose a definite time for the unfolding of the action expressed by the "gérondif" and you can even specify various times; see the example below.

Example (LPH’s)

• Averroès adoptera la méthode du commentaire littéral, suivant le texte d’Aristote, le divisant, en expliquant d’abord mot à mot les diverses parties, en fournissant ensuite des référence, et en dégageant finalement le sens.

As the extraction of the meaning from the texte occurs at the end of the application of the method and is a result of the bulk of this application you can transform the "manner" into a "goal" in English, which is more exact anyway.

Actually, I am going to completely disagree with LPH here. This is not a gérondif at all.

These are normal present participles and the en is a pronoun meaning du texte d’Aristote which would otherwise go after parties and sens

If these were gerundives, then there would be no justification whatsoever for having en expliquant and en dégageant, but only suivant and divisant. Indeed, if you add a "en" before these first two verbs, you find yourself wanting to ask very badly "…en expliquant les parties de quoi?"