What kind of scanner is this that it "requires access to the whole filesystem"
In most cases, the most that is needed by security teams is to check for vulnerabilities on the public or sometimes internal IP address, or for viruses, the later being (almost) impossible in a Linux based system, especially one that is a closed system with no external file repository other than Mitel.
Not trying to argue with you, but I have worked with government offices, security and fraud companies, international organizations, and no one has said they need access to the entire file system of a Mitel server before... I am curious more than anything.