Graeme, I can tell you that I have gone throuch the scenario you describe so many times.
If the FIA course believes that you should check all the installation, then apart from this being very difficult, it is also likely to be very expensive and also includes more than the BS recommends.
I'm all for raising standards, but people such as the FIA should try to understand how the real world of fire alarm systems actually operates.
I've never been impressed by third-party acredition organisations and similar. Whilst they purport to be raising standards, they invariably set unrealistic targets and add extra costs to the whole project. Are these extra costs worthwhile when there are other non-accredited service suppliers who don't need to add all the costs and can win more jobs. And as we all know, even accredited companies don't do everything right, every time anyway.
My view is that everyone would be better without BSI, NSI, BAFE, FIA etc. etc. If anyone is prepared to state that an installation complies to BS then surely this should be enough.
None of this solves the problem of a system that doesn't comply, however. No matter how you approach it, all your client wants is a certificate stating how marvellous everything is. There is no way around this, but you can soften the blow by letting everyone know in advance exactly how stringent your checks will be.