'In this matter' connects with the topic in hand. This being so, action being accomplished by the five causes stated, the man who, being without discernment, sees the doer to be only the self, pure and alone, that man, because his understanding has not been refined, does not truly see. By the teaching of the Vedanta teachers and by reasoning his understanding is unrefined; and even one who holds the self to be distinct from the body and the rest, if he sees the self alone as the doer, has an unrefined understanding too; so, his understanding being unrefined, he does not see the truth of the self or of action. He is therefore of evil understanding, of a vile, perverse, corrupt understanding which is the cause of ceaseless birth and death. He, even while seeing, does not see, just as a man with cataracts sees many moons, or sees the moon running when clouds run, or, seated in a moving vehicle, sees himself running when others run. Who then is the man of good understanding who sees rightly? The Lord says.

Thus, agency in truth belonging to the individual self with the supreme Self's consent preceding it, the man who, in that action, sees the self alone as the doer, he, of evil understanding, of perverse understanding, since his understanding is unrefined, since the understanding of a thing as it truly stands has not been brought about in him, does not see, does not see the doer as it truly stands.

This is a brief sub-gloss. For a fuller reading of this verse, see Madhusūdana, Śaṅkara, or Rāmānuja above.

'The pure one' is the actionless one, as that same text says, 'they call this the pure self because of its actionlessness'.