Guruji saw yoga as one. Different techniques for different people in different circumstances. But he was clear that what he was teaching was Patanjali Yoga - so any Hatha techniques he utilized were in the pursuit of that goal rather than vice versa. In fact, although the Hatha texts state that the purpose of Hatha Yoga is Raja Yoga and some passing lip service is paid to the angas of Ashtanga, the development of practice and practices as well as the the culmination of the goal are clearly significantly different.
Gerald James Larson, in his monumental Volume XII of The Encyclopedia of Indian Philosophies says:
"In addition to Patanjali Yoga, there are all sorts of other traditions (including Hatha Yoga) that use the word yoga in a different, non-philosophical sense. That is, there are a variety of traditions that are clearly influenced by Patanjali Yoga but diverge considerably from it. These traditions either explicitly disavow an interest in philosophy of Patanajali Yoga, or perhaps more to the point, choose to make use of some terms and practices of yoga for purposes that are quite often quite distinct from Patanjali Yoga. Moreover, they are all without exception sectarian religious traditions."
Larson goes further to say that this includes the Bhagvad Gita - one of the three important texts for the followers of Advaita Vedanta and one of Guruji's favorites.
Patanjali Yoga is generally regarded as a dualistic text influenced by or incorporating Sankhya philosophy, whereas the Bhagvad Gita is a non-dual text - a text of Advaita Vedanta. For Guruji there was no conflict. He saw sankhya and yoga as one - as is stated in the Gita. He also saw the advaita (non-dual) "evolving" out of the dvaita (dual). This he explained as the transition from the external limbs and extraverted awareness (dual) to the internal limbs and meditative absorption (non-dual). I think it is justifiable to say that the Sutra is both a dual and a non dual text: it utilizes our experience of duality and leads us to an understanding of the non-dual state (samadhi).
Pure Patanjali Yoga does not include the specifics of Hatha Yoga, but many elements can be inferred under the category of tapas. We know very little about what was said in the Yoga Korunta which is the text which puts Guruji's teaching in context, but he was not shy of quoting the Hatha Yoga Pradipika as well.
A cursory review of the Hatha Yoga Pradipika and the Gheranda Samhita will reveal how different these practices are from Patanjali Yoga (and indeed, from any yoga practiced in the West), and in the light of this, the end which the means provide must also be different. Even though the Hatha Yogis identify their state of realization with Raja Yoga - a term used to describe Patanajali Yoga, this state is not achieved by chitta vritti nirodhah but by a series of tantric practices.
Guruji did not prescribe a way to navigate the internal practices, he was much more concerned with establishing the external ones and creating a strong foundation. But he did prescribe a method for these external practices, at least for asana and pranayama and for him these fit very distinctly into the succession of eight steps which are Ashtanga Yoga.
We are left with a choice as to the content of our meditations. Some are religious in nature, some musical, some philosophical and some are inclined to extreme renunciation... for each individual there is a unique entry to the internal limbs of yoga.