Restarting my computer seems to have solved the security related crash but this also necessitates removing the existing Core Data store file as it complains the existing one doesn't match the model file.
[UPDATE]
Restarting does not solve the problem. But reseting the current version of the Core Data model file did the trick. I changed it to an older version and then back. This question helped me think of this as something to try. Using mergedModelFromBundles: and versioning (CoreData) Still not sure what the root problem is.
[ANOTHER UPDATE]
I put a file monitor on the .xccurrentversion file in my Core Data momd file bundle to observe when the file is being touched. I've noticed that XCode (or some build tool) updates the .xccurrentversion file periodically when XCode comes to foreground (either when the project is opened or when it's been in background for a while). When it did this today it updated the file setting _XCCurrentVersionName to the main momd file bundle rather than the version file. I replaced the .xccurrentversion file with an older version and it launched. This would explain why reseting the current model version fixes this issue. I have no idea what the conditions are for XCode to update this file.