Why? I don't think anyone knows yet.
The problem seems to be mitigated in some cases by moving the app manually to the /system partition, but this doesn't always work I don't think - for example Hangouts sometimes misses notifications for me and that's a system app. There's another nuance too - why do some apps not appear in the protected apps list (e.g. gmail)? That's not technically any different to Hangouts... is there a whitelist in the ROM somewhere?
Now I have my custom ROMs and deodexed ROMs, I'm going to be having a good poke around so hopefully we can fix this once and for all for all Honor / Huawei devices, but it would be super useful for anyone to contribute their findings so we can try and establish a pattern of behaviour while I look for clues.
PS: Topic also mirrored here at MoDaCo