But apparently ignored by many TOCS who just use the timing shown of the berth occupation
I'd be incredibly surprised if that's the case - most likely they use the times from TRUST which feeds a lot of systems and includes the offsets in the times reported. To see what they see just look at any site other than RTT that reports train running (I believe RTT uses its own custom offsets hence the times it reports can vary from the official version)
There are some problems with the official offsets, some of them are quite old and power doors and modern defensive driving do slow than station arrivals from older stock. Added to that, updating the very large number of them is a huge task and TOCs are not that likely to spot an offset which is reporting them arriving early - even errors the other way round, reporting later than actual arrival, are not easy to see and require a decent amount of work to show and get updated, just for one offset.
But I'd agree, especially as TRUST rounds down to a whole minute, that allowing 1' leeway in delay repay would solve a lot of issues and just be good customer service, but as with everything, it's very much not a conspiracy to pay out less, and more just a result of training and using data systems for purposes beyond those they were designed for