The issue isn't a technical one as much as a legal one. If the FBI can get the government to interpret the All Writs Act the way they want (any private entities must do what the govt says to aid a criminal investigation unless explicitly forbidden by law) to force Apple to write a custom version of iOS for them this time, the fear is that they can use the same law to install backdoors in ongoing versions. Legally there would be precedence for Apple to have to allow investigators to access other phones as well by means of making Apple write code to do so, which in the future could mean tracking location, turning on microphones and cameras, etc.