Finally seem to get a satisfactory answer to the question as well as the scriptural source for the Sloka.
Also,as anyone can see,its not surprising that the Sloka can very well be mistaken for a Sloka of Vishnu.
There is no way one can convince oneself that the Sloka is related to Ganapaty unless one sees the scriptural reference.
From the Vishnu Sahasranama found in the Skanda Purana-Avantya Khanda
Shuklaambaradharam Vishnum Shashi Varnam Chaturbhujam, Prasanna
Vadanam Dhyaaye Sarva Vighnopashaantaye/ Laabhasteshaam Jayatyeshaam
Krutasteshaam Paraajayah, Eshaamindeevara shyaamo hridayastho
( In his address to Devas, Lord Brahma invoked Shri Ganesha in the
Swarupa of Bhagavan Vishnu as wearing white and clean clothing
decked with four hands with a pleasing countenance and prayed to Him
to appease any type of obstacle in the task being initiated. May Lord
Janardana of Shyama Varna -blue complexion- who retains a splendid
blue lotus in his heart bestow boons to us as he is the Emblem of
Earnings and Magnificent Victories).
Edit-Further evidence that Sloka in question is just a pseudo Dhyana Sloka of Ganapaty.
The following (complete?) version of the Sloka is used for Visvaksena Puja.
śuklām baradharaṁ viṣṇuṁ śaśi varṇaṁ caturbhujam | prasanna vadanaṁ
dhyāyet sarva vighnopa śāntaye || yasya dviradha vaktrādyāḥ pāriṣadhya
paraśatam | vighnam nighnanti satataṁ viśvaksena tamāśraye ||
I take refuge in Vishvaksena who always destroys all hindrances, he is the general of the elephant
faced attendants and the numerous others.
That sounds quite reasonable to me since Ganapty is most often described in Scriptures as wearing red as opposed to white.
Also,almost all Dhyana Slokas of Ganapaty atleast mention one of the prominent features of Him(viz-big belly ,curved tusk,one toothed etc)in them.
In this case that is strikingly missing.No mention whatsoever of Vakratunda or Lambodara or the musika which is His Vahana.
The highest of Yogis meditates constantly upon Ganesha, with a single tusk, having four arms, holding a
noose, goad, the Benefactor, supporting the universe with his hands, having the mouse as his emblem, red
in colour, potbellied, fan-eared, wearing red clothes, anointed with red vermilion paste, worshipped with
red flowers, always attentive to the supplications of the devotees, the cause of the universe, the Unsullied
One who was manifested before the universe was created and existed prior to the manifestation of spirit
and matter-From the Ganapatyatharvasirsopanishat.