Sporran, I concur absolutely with what you say. In particular a regular issue here is people who have purchased separate tickets assume that those tickets have the same connection time and protection (should the inbound be delayed) that a through ticket has.
(There are some exceptions to the "separate tickets do not allow connections" rule as I found out recently. I flew BA LHR/CGH and then LA CGH/SCL on separate tickets and, because of a oneWorld benefit, I was able to through check baggage and get boarding passes at LHR but that's an exception. I digress)
Our OP here however, had purchased a through ticket and had even questioned the connection time with the selling agent. Now, it's possible the agency was at fault but having worked with systems like Galileo and Amadeus (which is what BA uses) I know only too well that some minimum connecting times published by the airlines can be (how can I put this) "ambitious". They work if the planes are on time and nothing goes wrong but with any kind of problem there is simply no margin.
As a for instance, many connections from the UK through US points of entry to US domestic points can have ludicrously short MCT. I've quite deliberately searched beyond page 1 of an availability (be it directly into the GDS or using a web interface) to find a connection that provides a safer MCT that the minimum the airline offers; in many cases I consider them unatainable. But I'm lucky, I've worked in the industry and seen (as you have) the results of broken connections and I take a conservative view. But Joe Public doesn't (usually) have our knowledge and takes what he is offered and then suffers when it goes wrong.
At least our OP had the sense to ask *and* to pay up to make himself feel more comfortable.