We've just been through the same process, adding a 14' x 14' extension to the rear of our house - exempt from planning permission as it comes in well under the size requirement etc.
In terms of gaining a cert of compliance, we've engaged an engineer, who's checked/overseen the process from the groundworks up.
IMO it would be hard to bring someone in at the end of the job to sign off on a cert when they haven't been able to inspect all aspects of the job - presumably now your RSJ would be encased in plaster?? And the new foundations are well covered??
Getting an exemption from planning permission however is different altogether, and can be gained at any time (assuming that the extension comes in under the requirements). Check with your coucnil planning office. It could be as simple as getting an architect to sign off a letter, without involving the council at all. As far as I know, you wouldn't need a compliance cert in order to be granted an exemption from planning permission - strange as it may seem...
To anyone else looking at adding a similar, small extension, or knocking a load-bearing wall etc., even if you're using a reputable builder and don't need planning permission, get an engineer involved from the very start.