The only other option is an Enterprise account from Apple, which will let you create an In House provisioning profile which lets people run your app without having to add the UUID. However, there are limitations. Apple's Enterprise Dev Program homepage.
We could not get a resolution from Crashlytics so switched to Parse.com. It seems to be working fine (will test further and post if any issues). We will migrate all projects to Parse as it seems to have a simple integration which works for multi-projects.