The DirectXTK has another function:
HRESULT CreateDDSTextureFromFileEx( _In_ ID3D11Device* d3dDevice, _In_z_ const wchar_t* szFileName, _In_ size_t maxsize, _In_ D3D11_USAGE usage, _In_ unsigned int bindFlags, _In_ unsigned int cpuAccessFlags, _In_ unsigned int miscFlags, _In_ bool forceSRGB, _Out_opt_ ID3D11Resource** texture, _Out_opt_ ID3D11ShaderResourceView** textureView );
to this function I can pass the required flags, as you said the D3D11_BIND_RENDER_TARGET and the D3D11_RESOURCE_MISC_GENERATE_MIPS.
I have created a DDS with custom mipmaps that differs a lot from the original picture, so I could clearly see that on a terrain. When I called GenerateMips the mipmaps from DDS has been hid by the generated ones (I think so ), so it means that it finally works.