Apparently the iGPU Multi-Monitor setting under advanced/system agent configuration/graphics configuration needs to be turned on. This is labelled for being for virtu but is necessary for the integrated GPU to be detectable by windows, even if you arn't running virtu.
Obviously the location of this may vary with different motherboard brands and the name of the setting may be different.
My guess is since lucid logix uses both GPUs, it tells the motherboard to simply run both - independent of whether you're running more than one monitor (with lucid outputting what you're rendering on the dedicated GPU to the integrated GPU), or using a multi-monitor set up taking advantage of both the IGPU and Dedicated GPU as independant outputs without lucid.
In my case this let me use my onboard video for a theoretical 3 additional outputs, rather than the switching that lucid does, and use quicksync alongside my discrete card.