If you can find any evidence (e.g. a benchmark) of a "good" brand card having higher performance than a "bad" brand card (ignoring OC models) I'd love to see it!
Custom coolers by far are much better than the reference blowers. Check out the 290x at launch, the reference design choked on heat until manufacturers were able to build their double/triple fan coolers on the platform.
Manufacturers have free reign on the designs of the cards, AMD has reference specifications but they have allowed full range of custom work allowed like switching out components for higher grade materials, different PCB bases so you can get more space or fit into a ITX build. AMD will never officially support OCing their products but that doesn't mean the manufacturers cannot market to that group of people.
Performance-wise theres really not much of a difference with fancier parts but instead you have increased reliability. You can safely push OCs at a higher speed without burning out the card or withstand being in a hot environment for a long time. Including that can also be a manufacturer's warranty, ones that trust in their products can even slap on a 5+ year warranty on their products. Its the same with motherboards, Intel and AMD provides the controller chips, everything else is free reign.
For my experience, i equipped an office with a mix of EVGA and ZOTAC nvidia cards. The ZOTACs had a higher rate of failure due to the shitty fans they used so i bought more of the EVGAs.