It is certainly correct to say that Vedas do not espouse a hierarchy of the Devas. There is no superior or inferior deity in the Vedas, as seen in RV 1.164.46, which you have mentioned.
Similarly, RV 5.59.6:
अज्येष्ठा ... अकनिष्ठासः ... अमध्यमासो
They have no elder, younger or middling members
Also, RV 10.72.4:
अदितेर्दक्षो अजायत दक्षाद्वदितिः परि
From Aditi was born Daksha, and from Daksha was born Aditi
यद्देवा अदः सलिले सुसंरब्धा अतिष्ठत । अत्रा वो नृत्यतामिव तीव्रो रेणुरपायत ॥
When the Devas well-connected, stood under the water, their dance stirred up intense dust.
Also, Niruktam 7.4:
... इतरेतरजन्मानो भवन्ति इतरेतरप्रकृतयः ...
They are born from one another, their nature or characteristics is shared
So, keeping the above deep philosophy in mind, if we look at the Puranas, when Vishnu is praised as the highest and Shiva is shown as worshiping Vishnu, in reality Shiva is worshiping himself. And vice versa.
Then why do such partial "sectarian" Puranas exist? The thought process can be gleaned from the great poet Bhartrhari's verse:
महेश्वरे वा जगतामधीश्वरे जनार्दने वा जगदन्तरात्मनि ।
न वस्तुभेदप्रपत्तिरस्ति मे तथापि भक्तिस्तरुणेन्दुशेखरे ॥
I do not see a metaphysical difference between Maheshvara, the Overlord of the universe, or Janardana, the Inner Soul of the universe. Still, my devotion is to the Carrier of the crescent moon (i.e. Shiva)."
It is the idea that among a roster of equivalent deities, we choose one that we connect with emotionally as our इष्टदेवता (iShTadevatA), our preferred deity.
So from the point of view of the scriptures, single Puranas are partial or "incomplete". Hence, all the Puranas and Itihasas are lumped together as "itihAsapurANam", because the Vaishnava and Shaiva Puranas complement each other, and when studied together, they "neutralize" each other and we get a neutral vision of reality.
From the point of view of practical faiths, Vaishnavism and Shaivism are just equivalent, because they both say that their favorite deity is the Brahman.