Q:

Does Yamunacharya consider Brahman as vibhuti of Vishnu? 

Gaudiya vaishnavas make a distinction between Brahman and Bhagavan. 
Let me explain the difference. 

In nyāya, the perception or cognition of a real object (dravya) occurs
  in two steps.  In the first step, the object is perceived separately
  from its attributes, and in the second step, the object is cognized or
  understood as possessing the attributes.  The first perception is
  called nirvikalpa pratyakṣa or indeterminate perception.  It is only
  when both steps are completed that one arrives at determinate
  perception of the object. 
Sri Jiva uses specific terminology to express the above concepts. 
  viśeṣya is an object without its attributes, or the object which is to
  be qualified.  viśeṣaṇa is the qualifier or modifier of an object. 
  viśiṣṭa is the qualified object. 
In the example of a ‘red rose’, the rose is the object, while ‘red’ is
  its qualifier.  The word ‘red’ separates or distinguishes the rose from
  the class of all roses.  This is one main function of the qualifier –
  to separate an object from others, and is therefore an essential
  aspect of definitions (although not all qualifiers perform this
  function; sometimes they are used to inform us of the attributes of
  the object).  The rose is the viśeṣya, red is the viśeṣaṇa, and ‘red
  rose’ is the viśiṣṭa.  
In the theology propounded by Sri Jiva, which he supports with copious
  references to scripture, Bhagavān is the viśiṣṭa, or qualified
  absolute reality.  The viśeṣaṇas of Bhagavān are His svarūpa śaktis.  If
  one insisted on separating Bhagavān from His viśeṣaṇas, then what is
  cognized is the viśeṣya, which is Brahman.  In other words, Brahman is
  Bhagavān without attributes. 
In the perception of everyday objects, the initial indeterminate
  perception of the object must inevitably give way to a determinate
  perception.  When we see a red rose, the first perception is not “this
  is a red rose”, but “this is something”.  In that first moment, we
  haven’t related the object with the class of objects possessing
  “redness” and “roseness” to arrive at the conclusion “this object is a
  red rose”.  In the next moment, however, we relate these qualifiers to
  the object, and cognize that the object is a red rose. 
Curiously, it is possible to have indeterminate perception of
  Bhagavān, and for this perception to persist eternally.  It is also
  possible to cognize Bhagavān, the viśiṣṭa.  Naturally, the perception
  of Bhagavān includes the perception of Brahman, just as indeterminate
  perception of an object precedes determinate perception.  
According to Sri Jiva, descriptions in scripture of absolute reality
  as “formless”, “without bodily limbs”, etc.  denote the indeterminate
  perception of the perceiver; words such as “knowledge”, “beauty” and
  so on identify the qualities of Bhagavān; and terms like “supreme”,
  “nourisher” and so on denote the qualified Lord. 

Chaitanya Mahaprabhu explains the verse SB 1.2.11 as follows in 24th chapter of Madhya lila of Chaitanya Charitamrita:

The word “Brahman” refers to Svayam Bhagavan, who is one consciousness
  without a second, and without whom there is nothing else. “ Knowers of
  reality declare that reality to be nondual consciousness, called
  ‘Brahman,’ ‘Paramatma,’ and ‘Bhagavan.’”  That nondual reality is
  Krsna, Bhagavan himself.  He exists in all three phases of time (past,
  present, and future).  This is evident from the scriptures. . . .  The
  word “AtmA” refers to Krsna.  His nature is greatness [b[hattva].  He is
  all pervading, the witness of everything, and the supreme form . . . 
  Although the words “Brahman” and “AtmA” refer to Krishna, by
  conventional usage they refer to the Undifferentiated [nirvisesa] and
  the Inner Controller [antaryAmi], respectively. 

That being said, let me summarize,
When scriptures talk about brahman without attributes, it is understood that it is nirivsesa brahman.  And when talked with attributes, it is referring to complete manifestation of Absolute Truth, Krishna.  
Another way to read upanishadic passages when Brahman is talked as having no attributes is that it doesn't have any material attributes.  
Jiva Goswami used both of these ways.  Baladeva Vidyabhusana doesn't use unqualified Brahman concept in his Brahma Sutra and Bhagavad Gita commentaries.  But, he uses it in his commentary on Laghu Bhagavatamrita of Rupa Goswami. 
Sridhara Svami gives support to some extent to these kind of explanation in his Bhagavad Gita and Vishnu Purana commentary. 
But, I came across interesting quote of Yamunacharya's Stotra Ratna. 
Atleast Rupa Goswami considered it that Yamunacharya considered Brahman as vibhuti of Vishnu. 
Here are the set of verses from Rupa Goswami's Bhakti Rasamrita sindhu:

2.1.188: “Who is that person standing before us, revealing a human form black in color, full of bliss, who covers even the happiness of
  brahman which appears spontaneously after the five types of suffering
  have been destroyed?” 
2.1.189: Another example from Brahma-saṃhitā [5.40]: “I worship Govinda, the primeval Lord, whose effulgence is the source of the
  nondifferentiated Brahman mentioned in the Upaniṣads, being
  differentiated from the infinity of glories of the mundane universe
  appears as the indivisible, infinite, limitless, truth.” 
2.1.190: “Thus the Śrī Vaiṣṇavas who have taken into account all the statements of śruti and smṛti, say that this brahman is the vibhūti of
  Bhagavān.” 
2.1.191: Thus it is stated in the Yāmunācārya-stotra [14]: “O Bhagavān!  The universe, and within the universe all the elements
  starting with earth, with coverings each ten times thicker than the
  previous one, the three guṇas, the totality of jīvas, prakṛtī,
  Vaikuṇṭha and brahman are all Your vibhūtis.” 

I know Sri Vaishnava commentaries on Gita and Brahma Sutras don't use unqualified brahman as I explained above. 
What do Sri Vaishnavas have to say regarding this verse of Yamunacharya? 

A:

Vedanta Desika clarifies the intention of Yamunacharya in his commentary on the Stotraratna. 

atra brahmaśabdena śubhāśrayanityavigraha upacaryate; svarūpaparatvokteranaucityāt।   iha tu -
"sālambano mahāyogaḥ sabījo yatra saṃsthite। 
  manasyavyāhate samyag yuñjatāṃ jāyate mune॥
  saparassarvaśaktīnām brahmaṇassamanantaram। 
  mūrtam brahma mahābhāga sarvabrahmamayo hariḥ॥"   
iti vaiṣṇavapurāṇe proktam।  catuśślokyāṃ ca, "mūrtam brahma tato'pi tatpriyataraṃ rūpaṃ yad atyadbhutam" iti।  atra brahmaśabdaḥ upacāra nimittaṃ lokottarabṛhatvam bṛhaṇatve   
In this context, term Brahma is to be interpreted as the eternal
  auspicious form of the Lord suitable for meditation
  (śubhāśrayanityavigraha also known as Divya Mangala Vigraha).  For the
  following is said in the Vishnu Purana:
(Wilson's translation) The supreme condition of Brahma, which is meditated by the Yogis in
  the commencement of their abstraction, as invested with form, is
  Vishńu, composed of all the divine energies, and the essence of
  Brahma, with whom the mystic union that is sought, and which is
  accompanied by suitable elements, is effected  by the devotee whose
  whole mind is addressed to that object.  This Hari, who is the most
  immediate of all the energies of Brahma, is his embodied shape,
  composed entirely of his essence; and in him therefore is the whole
  world interwoven; and from him, and in him, is the universe; and he,
  the supreme lord of all, comprising all that is perishable and
  imperishable, bears upon him all material and spiritual existence,
  identified in nature with his ornaments and weapons. 
In the Chatushshloki, Sri Yamunacharya's also says that the term
  Brahma is used to not only describe the auspicious form of Hari but
  also an even dearer form - that of Sri.  Thus the term Brahma only
  serves the purpose of an honorific here.