The subject of non-Nikaya/Agama Discourses is very complex. First, I think it is a mistake to view them as a unified corpus. It seems that they were written over a long period of time, among various groups, with divergent purposes. Some of them, such as the Diamond Sutra, appear to be very old. Others appear to have been written many centuries after the Buddha's passing.
In other words, I think it is a mistake to use a broad brush in describing them.
My sense of these texts is that they resemble, in many ways, texts on Jesus that continue to appear down to the present time. I don't mean historical works, but works that claim to present the teachings of Jesus, that the author has somehow accessed them and is now presenting "new" teachings. These kinds of works appear every few years; there is really quite a large body of such works.
I think that explains why, historically, Theravada simply hasn't had much to say about non-Nikaya Discourses. Just as dedicated Christian scholars do not spend a lot of time on the above mentioned kinds of works, so also I think that the Nikaya and Agama based traditions just didn't think that they deserved a lot of focus, commentary, and time. That's why one finds so little direct comment on them.
My two cents,