BP Nativization will not work with EDL enabled natively in all cases, but that does not mean that it cannot work. As far as reduced load times when EDL is disabled goes, remember that EDL was added a few versions ago so while disabling it does increase load times, these are how they were previously.
While disabling EDL is not a final solution to the issue, it should serve as a workaround at the moment but one thing to keep in mind is that, outside of one issue we experienced back in 4.15, all issues that have been reported that are caused by using Blueprint Nativization, EDL, or ASync loading in tandem have been content related and an error with the way the project itself is set up, so this may not be a bug with the engine and may require some reworking of your project.
If you would like assistance with this kind of issue, it would be best to provide a full log file of the packaging process and of the session where the crash occurred. This may give some insight into exactly what is wrong.