It seems pretty clear in the legislation to me? S5 by virtue of 5(1) (ab) - "any self-loading or pump-action rifled gun other than one which is chambered for .22 rimfire cartridges."
Note it doesn't mention either shotgun or rifle, only 'rifled gun'.
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I should have been clearer- I completely agree that the wording of the legislation should make it section 5. however the fact that these are sold and owned on section 1 certificates suggests that at least some police forces are allowing them. Granted my own FEO said i could have a section 5 gun converted to section 1 which is clearly against the guidance. That and speaking to another police officer who response to this was "yeah some police forces ignore that guidance anyway and interpret it differently". As such I'm guessing someone has either misread the legislation as "rifle" not "rifled gun" and decided it doesn't apply to a "rifled shotgun barrel" or noone has paid any close attention to the guns and so it has gone under the radar.
It would be interesting to know what the RFD would list the gun as when signing it onto a certificate. If they just put down section 1 shotgun then I guess the police would be none the wiser until someone asks the question.