I think when they moved to the M series they had trouble providing enough PCIe lanes. Not that I ever really trust Apple to ever offer non-proprietary storage again, but moving the storage controller to the SoC probably avoids any PCIe support they'd have to think about.

Moving the storage controller to the SoC makes sense for Apple because they already did the work for iPhone/iPad, and it reduces part count. Having no upgradeable parts inside probably also reduces failure rates. It's not the trade people here would make, of course.

Communication from the in-SoC NAND controllers to the NAND chips themselves is done through PCIe AFAIK