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Travel Allowance to Employee is it GST able Taxable Benefits ?

Hi There, 
We are in the process of designing the benefit package and would like to include the Travel allowance for people residing in prescribe zone A & B so that it could get captured in box 32 on T4 slips. 
and  employee can claim this items as lower of 3 for deduction in their personal return taxable income. 
We have referred various resources including employer’s guide taxable benefit and allowance and the benefit table. along with Section 6(1)(b) of Income Tax Act & not sure the treatment of Travel
allowance related to the GST aspects . 
Benefit guide Line Items says Travel Assistance in prescribe zone In cash where company i.e. employer is deemed to have collected the GST and accordingly Co. has to remit the same. 
which indicates that this GST Element is potential cost to the company in providing this allowance to employee. 
Further more benefit heading says GST is not applicable on Cash allowance….. So my question here is whether can company treat  this lum sum allowance given with bi weekly salary paycheck as cash allowance in the form of travel allowance. 
Concern here is the the scope of Deemed GST on this taxable benefit. 
and in case if company can’t avoid this GST cost then Is there any way to claim ITC or ITR on this deemed collected GST to ensure that whatever company remits can claim as input tax credit ?