Why does the Shabbat Rosh Chodesh Musaf have its own special text (Ata Yatzarta Olamecha Mikedem ...) for the middle beracha?
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I once heard a great Dvar Torah that I think is relevant to your question. I'll sum it up for you here and you can look up the sources if you wish.
We see a number of special minhagim related to Rosh Chodesh and Shabbat Rosh Chodesh:
An explanation for the above and some additional questions that I can't remember at the moment could be the Midrash that states that before the sin of the golden calf Rosh Chodesh was a Moed, meaning that there was Isur Melacha.