To the original question,to the best of my knowledge there is no 5th pod capability on an A340 or any other Airbus.
Regarding the Mexico City Tristar engine out ferry/ second failure incident , legend has it the captain got the serial number of the one working engine and personally wrote to RR suggesting they send it to Japan and get a few hundred copies made as it was the only one worth anything. Whilst his employers were reputedly somewhat chastened by his action it got results in the form of rapid delivery of numerous upgrade mod kits to sort out the early RB211's problems. I believe they were only ferrying from Mexico City to a nearby sea level airport for refuelling for another ferry flight back to MIA.
I once saw a DC10-30 two-engine ferry from South East Asia to Oakland California (Transamerica I think it was).
Regarding 5th pod certification, if you buy the standard 5th pod package from Boeing it normally only covers the model engines certified for use on that fleet of aircraft however as noted by several posters if you spend extra bucks you can get other engine models included but it usually involves a dedicated test flight to check buffet, trim required etc and a revised Flight Manual supplement.