That's only my experience on the R9 280. Nvidia card (or other AMD card) may be totally different. Also, I only realise this is EFI related in El Capitan.
I upgrade to dual GPU after upgrade to El Capitan, and I need to boot without EFI for reliable crossfire setup in Windows. Therefore I may leave the switch at the non EFI position and end up no audio via HDMI.
So, there are few variables here.
1) Multi GPU setup (the 2nd one is the 7590, effectively the same GPU as R9 280)
2) OSX version (this EFI sensitive behaviour may only happen in El Capitan
3) GPU model, I can only confirm R9 280's audio is EFI related.
So far, I can simply flip the switch to alter the HDMIAudio behaviour, so, I assume EFI is the main factor (or the only controlling factor).