One of those articles on motogp.com that you wish had a bit more detail. Maybe Krops will fill in the blanks.
http://www.motogp.com/en/news/2014/Comparing+engine+usage+in+2014
Scott Redding (GO&FUN Honda Gresini) and Nicky Hayden (Drive M7 Aspar) went up to their 11th engine, while Hayden’s team-mate Hiroshi Aoyama was the only rider to use his maximum 12
Were there actually 12 engines? Or is that 6 engines that were built, refreshed and sealed 12 times?
It also raises the question, if the Factory Hondas can survive only 5 engine in a season, why did the lower spec, lower stressed Open Hondas need 12?
So for the second part of your question there are 2 factors here. !- the open class bikes are actually more stressed than the factory bikes. This is due to the unlimited funding nature of the factory class. The guys from Honda and Yamaha can throw as much money as they want at their riders and give them the best of the best. Where the open class guys have to buy their parts from Honda and Yamaha, therefore not getting the latest and greatest, while also doing this on a budget compared to the factory options.
Secondly the open class gets 12 so the can continue to develop the engines. Meaning the can play with engine set ups, parts and tuning options to make them faster. This may cause an issue or two and they can actually lose more engines more quickly this way.So the engine counts are set to make MotoGP more competitive for all of the riders.
Hope this helps and doesn't over answer your question........This is just what MotoGP did this year to try and make things more competitive for all riders and bikes.......It can go much deeper into other things they have changed, such as how much fuel the open class bikes can use vs. how much the factory bikes get.
I only ask because Dorna was pointing at WSB and Aprilia/Ducati in particular and saying "Look how many engines they're using, it's ridiculous" when what they were really talking was how many refreshes they had.
Knowing exactly what each team/rider has in their garage is probably not going to be common knowledge........I believe this for various reasons and if you would like to talk about them I would be happy to, but don't think the information for individual teams will be easy to find.
http://motomatters.com/analysis/2014/02/28/motogp_rules_primer_open_vs_factory_the_.html