To clear a few things up, FENSA aren’t the only competent persons scheme you can use for replacement windows and doors, others are available.
Also, your local authority can, and should accept an application for replacement windows and doors, which you need to submit prior to commencing works, they will then inspect the works as with any other building regulations application, and issue a completion certificate all being well, this has exactly the same legal standing in terms of demonstrating compliance as a competent persons certificate, or regularisation certificate.
Windows and doors are classed as ‘controlled services or fittings’, hence their replacement requires building regulations. The only thing you can do legally without notification or using a competent person is replace panes of glass, and repair casements/frames/doors.
Competent persons schemes are only valid where the replacement of windows or doors involves No alteration to the existing opening. Once you touch the wall/lintel it’s a building regs application only job.
I don’t use the wrong people, I work in building control, and have to regularise windows and doors every week because house sales are being held up by lack of a certificate.