I think the issue that they are trying to make is that there are modern ways of protecting the keys with hardware level security, that aren’t being used. As someone who works in AppSec this is all too common. All it takes is one library in an application to be popped (doesn’t have to be signal), and security keys end up leaked. If it isn’t already, I’m sure that signals keys will be included in exfil scripts.
Tools like TPM and SecureEnclaves (TrustZone,etc) mean that malware, and other nasties have a higher bar that they need to meet.
I'm not surprised... I think people ('the ones that care at least') would be horrified to know how much of this stuff slips through, because it's hard (there are so many other things that are pulling at developers that something falls through the cracks). Most of the time the right answer is to bring it up. Then thank them when they resolve the issue (with beer and pizza money at the very least).