"My question is - are there any other failure modes which could result in the same configuration again? How well, for example, is the tandem engine configuration protected against an uncontained engine failure and collateral damage to the undercarriage (even with armoured pipes)? How well is the wheel area protected against a major bird strike on the two engines. ( Remember the E3A at Elmendorf?)"
Most big-iron aircraft that fly today have risks associated with the "what-ifs" you pose above. These risks are addressed by the design regulations under part 25 and part 33 that presume mitigating factors are present in the design. The regulations were preceded by the design of the Concorde, however important precedent setting design conditions were imposed on the Concorde to address these risks in an even more thorough fashion than the more general regulations of today.
As in most cases following an accident some weaknesses and vulnerability may be found in hindsight, that were not obvious in the initial design assumptions, however stringent they might have been.