I once read that most of the popular collective nouns were all coined during something of a fad for the idea of them. Previous to that, there were some that more or less arose organically, and when the need arose for special cases. But as more scientists and naturalists cottoned on to their existence, and that there were even some whimsical ones, a kind of Cambrian explosion of them occurred. There was an arms race to come up with the most fanciful and poetic collective nouns. But none of these more artificial examples had a need for their existence which would warrant their continued use, so no one did. Except in cases which you mention, pointing out their oddity.