I don't think people repainting and such are nessicarly "Fixing" a toy, just modding it to their likes. The problem is when they go around claiming to have "Fixed' it, that I feel it becomes a problem.
Part of the difference is that those covers are primarily one person's art. Sure, you probably have an inker and a colorist, but the lines and composition are one person. A toy however is a team design at pretty much all levels.
J Scott Campbell recently had his Spiderman cover "fixed" by someone online. A few weeks ago, someone on twitter "fixed" someone's Sonic the Hedgehog fan art where Sonic, Tails and Knuckles were drawn as humans. Both times and other times, the "fixer" gets called out and criticised as you shouldn't go around "fixing" someone else's art because its rude and disrespectful to the original artist. And I was thinking isn't "fixed your s*** for ya" exactly what toy customisers do?