Re: Yes but...
The security holes come from the software, not the hardware which is basically just a DSP on steroids, so if they had control of the software they could make it secure (well, they could try, but no software that complex will ever be bug free...)
The choice of Intel wouldn't have been "oh Qualcomm leaves in backdoors, let's go with Intel because they don't" it was more "Qualcomm used to be our only option for a standalone baseband, now Intel is in the game too".
There have been rumors they've been talking to HiSilicon, who doesn't have a standalone baseband today, but would presumably be willing to offer one if sold at Apple's purchase volumes (even if only for the Chinese market, and their special TD-LTE and TD-SCDMA flavors) HiSilicon also might be willing to license the IP, giving them another alternative if Intel proves unwilling to do so at a price Apple considers reasonable.