This is just my understanding that might be incorrect.
As you posted in this articular thread the bat must be pre-RCR so is not in scope, as long as the OP conforms with the BSS there should be no problems.
The core of the RCD/RCR boat documentation seems to be the boat manual that should (but from what I have heard often does not) give the full details of all the equipment and fit out, showing how they meet the various clauses. This is probably easiest done by complying with the relevant ISOs, in which case it will be deemed to be compliant. Otherwise, the builder will need to prove that their solution does meet the regulations.
If the boat is completed with a full manual, then the cost of getting the certificate should be minimal. One way of ensuing it does meet the ISOs is to work with a surveyor throughout the build, exactly as you describe. I am not sure if a DIY builder can still apply to the RYA to get the certificate, but at one time this was possible, but presumably the RYA would need to see adequate documentation - the manual.
The manual should have a full wiring diagram showing cable sizes and colours etc. Likewise, one would hope that a similar specification or diagram for the gas system would be included, as would the domestic water system if that alls under the RCD/RCR.
What should be provided and what is provided do not always seem to be the same.