Patents are the main thing here.

Building a cellular modem, complete with working protocol stack, entirely in software has been done as a 1 person open source project.

Making a production -ready modem is clearly more complex, but far from hard for a company with the resources of Apple.

However, doing so whilst not violating any of qualcomms huge array of patents is the real challenge.

I'm willing to bet that the release date of this phone probably closely aligns with the expiry date of a patent they couldn't work around.

It is extremely hard to design a modem like this. Just the ADCs and DACs you need are like 2-3 year development and 1-2 year testing before going into production.