Actually, you are quite correct: some do build to full compliance and have their work regularly checked. All should. So something for new boatowners to factor in their decision-making.
"WHY don't customers go back to the builder at that stage, if it's a non-compliancy issue from the start?"
I think there's two issues at play. The first is the RCD and the BSS have a small number of conflicts set up within them. A boat is built to an RCD, but maintained by the BSS - so you have to go with the first even though it won't be acceptable to the latter. Also, rules change from time to time: so four years post-build something that might have been previously acceptable no longer is.
But when the Boatbuilder cannot claim either of these issues as pertinent that is where the real trouble begins. For many I've spoken to on this issue, the reality has been paying to get it fixed versus having to take a boatbuilder to court to enforce their consumer rights (in cases of dispute). Unless the boatbuilder is a member of a Boatbuilding Association, which can assist with arbitration, there is no other organisation to enforce your legal rights, aside from the courts.
Ultimately, resolving one's BSS issues is much cheaper, much less stressful and not nearly as time-consuming. Remember that if the boatbuilder has gone out of business (even if they've restarted under another name) then the law states that you cannot make any further claims against the company, unless you can prove the directors have been negligent (again a very expensive process). This applies to Ltd companies, not sole-traders. So it's a case of making the best of a bad bunch of options.