And did the sky fall in?
No, but Jack probably fell out of his chair .....
When pilots in the current system call on ATC frequencies to file flight plans and ammend them does this effect safety
As you well know, there are no such things as "ATC frequencies".
There are frequencies
used by ATC to provide services, including Class G FIA (Flight Information Area) frequencies. They are
not "control" frequencies, where separation services are provided. It is entirely appropriate - and required in the scenario outlined in the NOTAM and AIP - to use FIA frequencies for their intended purpose.
To
not use or monitor FIA frequencies when appropriate and required could cause a nasty situation, given the wrong circumstances.
Whether an FIA frequency is retransmitted onto other frequencies by Airservices is irrelevant to pilots, and not a reason to not use it or ignore the rules.