I think the underlying problem is that the apps stop talking because the certificate validity check fails when traffic is proxied through your MITM. No MITM proxy can make that succeed, but if you can control the CA store that apps read, then you can create a certificate, add it to the trusted roots, use that cert to sign a certificate for someone else's website, and then when the app uses the system library to verify the validity of the certificate, it will appear valid, even though it's not. Without being able to hack the certificate verification, you can't MITM traffic between two devices you own. I think that's the complaint the grandparent has.
Apps can still pin certificates, of course. At that point, you have to exploit the app's other faulty assumptions like "I'm running the same code that the compiler produced" or "writing 0 to memory address 0x12344321 and then reading memory address 0x12344321 will result in reading 0", which are straightforward to make false. Though probably not on a stock iPhone.
I would bet that > 75% of the top 50 apps use SSL pinning. Apple makes it really easy to do and it's an obvious first defense against reverse engineering.
What happens is that apps don't work if their cert is issued by another CA, eg. "we only use digicert so any other CA issuing us is either attacking us or a enterprise/hobbyist MITM which we don't care about anyways".
Apps can still pin certificates, of course. At that point, you have to exploit the app's other faulty assumptions like "I'm running the same code that the compiler produced" or "writing 0 to memory address 0x12344321 and then reading memory address 0x12344321 will result in reading 0", which are straightforward to make false. Though probably not on a stock iPhone.