Well.. the point still stands that screw attack is not invulnerable to everything; if touching Mother Brain or Ridley's tail is enough to break screw attack and hurt Samus, I would suspect that assaults from Dante's blade would probably be able to break through screw attack and do comparable damage if not vastly more. This especially notable when taking into account that that the enemies, even the bosses that I mentioned are not, to my understanding, of a magical nature comparable to the demonic hell spawned powers that Dante is made up of. That is unless someone can enlighten me to the magical nature of Ridley's tail other than that it is a spearhead like weapon attached to Ridley's backside.

As far as Chozo involving a lot of ancient magic, the "Chozo lore" that I have read from Metroid Prime does not seem to give a strong impression of the use of magic in their technology.
For those of you who would like to read the "Chozo lore" all layed out here are some links:
http://www.norfairdepths.com/chozolore.htm
http://faqs.ign.com/articles/384/384481p1.html
Reading the lore, it seems as if there is a clear distinction between spiritual (magical) and those of technology. There is even a later display of some resentment towards that which is science and technology, and it would seem the Chozo chose to "abandon" technology and look towards being more spiritual and "natural" and concentrating more on "simplicity" (which seems to be equivalent to avoiding the use of advanced technology). I would even say that their spiritual abilities did not seem to develop until after they abandoned technology that they developed any real spiritual advancement (mostly evident in "harmonization" in the second link)
This is of course only my own opinionated interpretation, but it seems that when the "Great Poison" comes, technology has failed them, and they begin to look to spiritual means and the hope that it provides in order for some kind of salvation.