IMO, there is no extra risk to run a card at stock config (unflash). Everything as per factory setting, nothing should go wrong. Either the card work or not.
On the other hand, a flashed card means the ROM has been modified. There is no guarantee that the card can work properly. So, install a flashed card should have higher risk.
For AMD card, it's just the matter of boot screen, or card's ident inside MasOS (cosmetic).
For Nvidia card, it's the matter of boot screen, and PCIe speed (ONLY in Windows). No idea why Nvidia provide a driver than can allow unfleshed cards run at PCIe 2.0 in MacOS, but not in Windows. But if you run a unfleshed Nvidia card in Windows. The card can only run at PCIe 1.0 speed. Base on my own test, and few other review. That virtually nothing for most mid - low level card in gaming. But if you are running the very high end card, or doing some GPGPU that very bandwidth sensitive. This extra limitation may cause issues.
There are few advantages to flash a Nvidia card
1) provide boot screen, which means the user can use boot manager.
2) provide basic display when Nvidia web driver is not yet installed / activated in MacOS (for Maxwell and Pascal card). Without this function, the card will display nothing at all, which makes the user much harder to install / activate the driver (e.g. via remote control). And this is the ONLY way to access recovery partition with an unsupported Nvidia card. Also, the user can boot to single user mode in order to diagnosis / fix some issues. Without this function, the user may only able see a black screen but never able to read the error message.
3) Allow the card run at PCIe 2.0 speed in Windows (we already discuss this)
http://www.guru3d.com/articles_pages/pci_express_scaling_game_performance_analysis_review,9.html
As you can see in this link (thanks BillyBobBongo), the difference for GTX 980 is virtually nothing, only 1-2 FPS (which is true for most of the games).
However, I will assume the 980Ti or 1080 is already the limit. Which may already shows more FPS drop on more games, and once go beyond that, the PCIe 1.1 limitation should become more significant.
Definitely not, these cards' power requirement is so low. The cMP can drive them easily without any external PSU.