The core m3-7y30 has a listed tray price of $281 - 74% higher than the $161 of the 4415Y. While MS is likely to get some serious rebates on chips compared to tray list prices, there's no way they'd get the m3 into a $399 tablet.
As for the 4415Y, it's a Kaby Lake part, not Atom based at all. That's Pentium Silver you're thinking of, not Gold. The m3 would no doubt be faster (1GHz higher turbo, twice the cache), but also significantly more expensive. I'd rather take the cheaper tablet, thank you. Besides, MS already uses the m3 in the entry-level Surface Pro, and it would be an odd choice to put the same CPU in a tablet at half the price of that with the same parts. If anything, that would force the price for the entry-level Surface Pro down by at least $200, which is definitely not what MS wants (as that would tank sales once they launch an upgraded model at what would then be an effective $200 price increase).