He wasn't working in a security role, so that would not have been a concern for whoever made that decision.

Other government agencies that do actually have people in security roles will be less inclined to issue iPhones.

This case sets precedent, that's the whole point.

But Apple is only able to do anything at all because it's an old phone without security features present in later models.

Also, any other manufacturers' phones would be trivially hacked in the same case, because the firmware can be overwritten without needing to be signed. Apple is pretty much the only one that requires signing.