Here is what Alan Wallace says in 'Stilling the Mind' (p 62) - I think this speaks to your question:
"Visualizations are fine. The stage of generation is important. Yet you must still confront your mind; you have to go right through it. That is taking the mind as your path. You need to go to the very ground of the ordinary mind. This requires shamatha. You don't need vipashyana for that nor Dzogchen, nor bodhichitta. But you do need to go right to the ground of your ordinary mind and let the mind settle, unforced. When the mind is quiescent — no turbulent thoughts or emotions arising — it is relaxed, still, luminous, and free from effort. That is shamatha."
The "ground of the ordinary mind" is the substrate consciousness; and shamatha is the essential practice for realizing this ground. Of course we don't want to stop there. I understand the visualizations of the stage of generation practice as a way to keep our eyes on the real prize: 'piercing through' the substrate to realize rigpa (pristine awareness) for the sake of all mother sentient beings. This is important to cultivate from the outset, considering how attractive and seemingly ultimate the experience of shamatha will be. But we must keep going to realize our deepest aspirations. Dudjom Lingpa teaches that stopping in the substrate "does not bring you even a hair's breadth closer to the paths of liberation and omniscience."
[Sharing this without any special authority, but as a grateful fellow student of these teachings. I welcome any corrections to this answer.]