As I understand it Apple don’t have a very fine-grained trust system unlike Microsoft. Remember that crt.sh is only a service from Rob at Comodo, it’s not an official communication of any trust store’s policies, and Apple might internally have some mechanism that makes certificates issued by LE not work for these purposes, but equally they might not.
Although there are a lot of X.509 certificates in the world, my personal opinion is that in terms of public systems only the Web PKI (ie for TLS certificates on the public Internet) is subject to any real weight of oversight. So, if you can be trusted in the Web PKI, that’s good enough.
In the SHA-1 exception process all the payment suppliers basically keep saying, well, probably we should have some sort of trust relationships for financial stuff, but we’d have to agree what the rules were and we’ve never gotten around to it, so actually everything basically depends on the major Web PKI trust stores, Mozilla, Microsoft, Apple and Oracle. Some proprietary backend systems aren’t tied to the Web PKI, but a huge proportion of financial transaction stuff is.