If they believe that uncontrolled 3rd-party clients would make it easier to breach their protocol (because they know their protocol's weaknesses), it would make sense to be openly hostile to 3rd-party clients.
If there's no third party client then the e2e is completely moot because Signal could be forced to push a backdoor to their customers and they would never know e2e has been removed.
How would a third party client make it easier to breach the protocol? You can still study the source of the client, the protocol, make a fork of it and modify it, etc. The official client is fully open source.
The argument for security for disallowing other clients would be being able to modify the protocol to patch out security issues without worrying about compatibility with other clients.