As far as the Mario enemies thing and whatnot, I don't know of any in-game source up until now (I haven't played a lot of the newer Mario games except for the 1st Galaxy game, 3D Land, and New Super Mario Bros 2), but I can say that I know of one possible (non-canon/fanmade) explanation that not only kinda makes since, but is entertaining to say the least is this: http://brawlinthefamily.keenspot.com/characters/reario/

I can't commit on RE2 as I never played it for more that a few minutes (I couldn't get used to the controls and died when I started the game the first time. sad, but true)

The Sonic games: Eggman/Robotnik thought it was a good idea to make machines that not only leave him mostly vulnerable to attack, but also are easily destroyed upon him taking a set amount of damage, but the machines themselves were never attacked. This is true for (almost) every boss fight he is in (among others)