If you try installing the latest eShop on the N3DS while still on 9.5 emunand and using anything OTHER than GW, the title will not boot because it is expecting to see 10.0, not 9.5. It actually just sits on the back screen with the red 3DS logo.
GW doesnt have this problem because of the way it handles spoofing the firmware to play newer titles on lower firmwares. Not sure what they are doing, but whatever it is, it's something that CFW devs haven't figured out or at least been able to get working reliably enough to add it.
NVer installs just fine and is, in fact, the only solution for signing into NNID on CFW with the N3DS atm. I supposed installing both NVer and CVer would allow the latest eShop version to boot, allowing CFW users to just use FMP, but tbh the fewer oddball title versions you have to install the better.