Apple responded to my report with the following:
This will need to be resolved by the server administrator. We have upgraded the proposed ciphers in L2TP IPsec VPN to also propose SHA-256 for the Child SA in IPsec. The issue seems to be that the server is accepting SHA-256 cipher for the child but maybe dropping the ESP encrypted packets with SHA-256 HMAC. This maybe because the server is assuming a SHA-256 HMAC with 96 bits instead of the standard 128 bits. Switching the SHA-256 HMAC output from 96 to 128 bits should fix this issue.Thank you for your feedback. I have now disabled the SHA-256 compatible mode (96 bit) on my VPN server and now it works.