You have this problem with chrome and ie, too. I do not think its an pc/mac/somegear problem either: That tiny little missbehavior anoys me for years. Finally i just decided to do something. The recently read google hits refered to an osx enviroment. Those guys thought it would be a mac problem.
To those who might read this and have any technical background: my guess is, that this problem with a browser plugin (flash player) is identical to that problem a regular applications (or '') havappse. Best example would be antivir, catching focus to show up the own comercial window after updating. As i use antivar exclusive for private concerns, that keeps minimizing my fullscreen game-'window', which causes game crashes in some case.
In the case of antivir it is not necessarry to catch focus at all. For setting up the plugin within th browser 'sandbox' and keep playing the vid it might be essential. However - i can speak only for regular windows apps - when it were my app stealing the focus, i have no system build in chance to give the focus back to that application the user expect to process his input. Even giving it back to those apps my app stole from is not an easy option.
Even all those browse extensions are called 'add-in', most likly the word in has nothing to do with it. Anyone building an add-in would keep the process-logic capseld outside of the brwoser to work with i.e. the jre and providing only a minimal interface in the code of the add-in for displaying issues. Otherwise you could build seperate versions of process logic for each browser on top to the system issues - just compare watching youtube video on iphone and on android.