Was deed of Indra demolishing 3 cities a source for the story of destruction of (3 cities) by Rudra?

The devata of Rigveda tenth mandala 47 and 48 suktas (hymns) is Indra Vaikuntha. This is not Vishnu but one of the incarnations of Lord Indra. He is named as Vaikuntha because of his mother Vikuntha, daughter of Prajapati.

There is a text called Bṛhaddevatā which is written by Sage Shaunaka. This text contains the details of the deities worshipped in hymns of Rigveda. It also gives the background stories of composition of the mantras.

There is explanation given for these hymns.

There was an Āsuri, daughter of Prajāpati, Vikunthā by name. She, desiring a son like Indra, performed very severe austerities. She then obtained from Prajāti her desires (in the form of) various boons. And Indra himself was born of her, as he wished to slay the Daityas and Danavas. Once he was engaged in battle with the Danavas.

Of them he slew nine nineties and seven groups of seven. Having shattered with the might of his arm the citadels of gold, silver, and iron, (and) having slain all (of them) in their respective spheres (yathāsthānam), as arrayed on earth and the other (two worlds). On earth he exterminated both the Kālakeyas and the race of Puloma, the archer, and in heaven the notorious (tan) offspring of Prahlada.

 Now a question arises - Was deed of Indra demolishing 3 cities in the above story,  a source for the story of destruction of (3 cities) by Rudra?

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Rig Veda mentions purandara - पुरन्दर (one who destroyed cities). Rig Veda praises both Agni and Indra as purandara - पुरन्दर.

In praise of Agni: Rig Veda VI.16.14

तमु त्वा दध्यङ्ङृषिः पुत्र ईधे अथर्वणः। वृत्रहणं पुरन्दरम् ॥१४॥

tamu tvā dadhyaṃṃ ṛṣiḥ putra īdhe atharvaṇaḥ | vṛtrahaṇaṃ purandaram ||

In praise of Indra, Rig Veda II.20.7

स वृ॑त्र॒हेन्द्र॑: कृ॒ष्णयो॑नीः पुरंद॒रो दासी॑रैरय॒द्वि । अज॑नय॒न्मन॑वे॒ क्षाम॒पश्च॑ स॒त्रा शंसं॒ यज॑मानस्य तूतोत् ॥७॥

sa vṛtrahendraḥ kṛṣṇayonīḥ purandaro dāsīrairayad vi | ajanayan manave kṣāmapaśca satrā śaṃsaṃ yajamānasya tūtot ||

If we closely observe, both Indra and Agni were praised as eliminator of Vritra and destroyer of cities.

That is the beauty of above mantras, composers of which were different sages, of Rig Veda. 

They are referring to the same Almighty or BRAHMAN, because Agni, Indra are epithets used to indicate same brAhman (RV I.164.46 - ekam sad ...)

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Coming to the destruction of 3 cities by Indra, as mentioned in Bṛhaddevatā of Sage Shaunaka, we can infer from the above that Sage Shaunaka explained the deeds of Indra as mentioned in Rig Veda, in an anecdote .

Destruction of 3 cities or Tripuras by Rudra, as mentioned in Krishna Yajurveda, might have followed the anecdote of Bṛhaddevatā of Sage Shaunaka.

One interesting aspect is that Vishnu is also called purandara in Vishnu Sahasranama No.335

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The term puram is also used to refer to the three Sariras viz. the sthula,sukshma, and karaNa sariras. 

He is purandara because he has torn apart these three and releases  the Atma beyond these three Sariras.