Sure it will, but it will whether it's powered by Intel or not.
The underlying "disruption" will happen whether or not Intel helps these chips get a few hundred extra megahertz in clock speed. I think Intel needs to profit from it as best as it possibly can.
Ideally Intel would do a good job with Atom and grab market share with its own solutions, but since they seem unwilling/unable (you can pick) to do this as we've seen from years of failed execution, why not profit from it by playing foundry to select customers?
I wouldn't fab for a company like Qualcomm since Qualcomm is a direct merchant chip competitor. But it could make a lot of sense to fab for companies that wouldn't buy a merchant solution anyway like Apple, LG, Huawei, etc. especially at the high end of the market.
I think in the low-end and mid-range, where companies are less able to afford to do their own SoCs, competing hard with merchant solutions is the right way to go. Intel can do this with x86 or ARM, honestly doesn't matter, but I think Intel-branded/designed SoCs are best for these segments, not foundry for other chip designers.