yveid - if you have proof that an unlicensed engineer was not supervised by the engineer of record, then report them to the licensing authority. I have no personal experience with that in the UK, but I'd be surprised if it's significantly different from most US jurisdictions. If you don't have proof...then please stop throwing around unfounded accusations of unethical behavior. I doubt you want to be called a lying cheat behind your back, and neither does that engineer. Contact the engineer of record (in the US we have to affix our professional seal to the drawing, so even if my subordinate did all the work my name would still be on the drawing) and ask them about it if you're unsatisfied with what you're getting from the design engineer.
The engineer set the bearing depth to a suitable level based on the information he had. The only information he had was that there was fill in the area several feet deep, and you needed to get below that. If the contractor failed to get approval for a variation, it's his own fault even if it was justified.
This is a house. While I agree that it deserves due attention to ensure its safety and reliability...economics are economics. Usually the best way for a structural engineer to provide that and not lose their shirt is to be conservative. I'm much more conservative on houses than I am on commercial construction. For one thing, homeowners tend to sue more. For another, the contractors tend to be significantly less competent and more prone to ignoring the design and screwing things up. (Not all, mind you - I have a few residential clients who are absolutely top notch and I would gladly have them build my own house.)
This is not something that can be resolved by a bunch of anonymous strangers on the internet. Figure out what needs to be done for the EOR to approve it, or find somebody who will take over the roll of EOR who will approve it.