[The Squatter of Amon Rûdh]

I think you may mean HME XII: 353ff. Looking at the notes to the text, it would appear that the account you mention forms part of some untidy notes for an excursus on names at the end of The Shibboleth of Fëanor. It does paint an excellent portrait of Fëanor's unreason, and I can only imagine that it was omitted because of its reliance for some of its effect on Amrod's mother-name, which is clearly a 'name of insight', given its context in SF. The account in HME XII does skip suddenly from the naming of the twins to the burning of the ships, which would mean that to incorporate it into The Silmarillion would have meant separating the vital discussion between Fëanor and Nerdanel from the later account of the tragedy at Losgar, possibly even omitting the former entirely. The irony that derives from Fëanor's desire to change his son's mother-name and his subsequent fulfillment of its prophecy would certainly be lost given such a decision, and perhaps CRT simply wanted to avoid such a mutilation.

Another, less likely alternative would be that during the composition of The Silmarillion, CRT had simply failed to notice the account, contained as it was in a text which he describes as "confused and confusing", and which was originally hand-written at speed. This seems tenuous to me, but perhaps he confused these sheets of manuscript for an excursus on the meanings of names (which was their original purpose), and simply set them aside, only to discover the story they contained at a later date.

Having said that, I don't presume to know what CRT was thinking at any given time unless his own notes announce it. I have no information that can't be found in HME, and the above is simply wild speculation on my part.