As of Windows 8.1, hybrid GPU configurations are officially supported by the OS, so this whitepaper is somewhat out-of-date. For D3D9, you are correct that your only choice is one or the other, and that the decision is made outside of the control of your application, but for DXGI (i.e. D3D11 or D3D12) there is no adapter hiding. The only thing that those exports will do is change the default enumeration order of the GPUs. Which, if you're enumerating explicitly, doesn't matter too much.
I'm going to take this to mean that DXGI does the right thing in various hybrid GPU configurations, as long as you are running Win 8.1 or beyond. If someone has up to date info and I'm wrong, please correct me, but the last time I dealt with this DXGI does not do the right thing in D3D11 under Win 7. In an Optimus setup, it would report the Intel adapter with displays correctly, and then report a second adapter with zero displays and nearly no adapter information. Unless I did extern the variable as outlined in the whitepaper, and then I got the enumerations I expected. Has that behavior changed?
I guess my point is, unless someone has more current info that my experience is no longer what happens, you might want to still handle the case for D3D11 users not running Win8.1+?