In cases like this, where the upstream of some of Cloudflare's servers is known to be non-transparent (dropping or modifying data going through it), couldn't they tunnel everything to Cloudflare servers with a working upstream, and connect to the origin servers from there? They would still benefit from caching near the users, while avoiding the broken upstream.
The lesson learnt from this fiasco is that CF can't trust its upstream ISPs, so tunneling traffic over to another ISP in a different geo adds additional overhead without actually solving the problem.
The right approach to fix upstream MITM is to drop http+https mix and match mode.