This sounds like a general amount paid to staff who need to regularly travel to Site, such as being paid a 'car allowance' per year of £X,XXX. The fact it is categorised as 'taxable' means that it is likely to be a general payment (classed as income) rather than a reimbursement of specific travel expenses.
If your contract stipulates a different fee percentage for items 13 (a) travel and 13 (b) subsistence and lodging, then it could be included under 13 (a), and so be subject to the lower fee percentage.
The only issue, especially from the Contractor's point of view, is that as the payment is 'general' (not specific to a particular project) and further classed as income (taxable), then it should be included as part of a person's salary under item 11, or possibly a 'special allowance' under 12 (d).
Like most discussions, it depends on what the value of the outcome is which determines how much time and effort you spend trying to 'get it right'.
If there is an element of ambiguity created by the amendments (different fee percentages) then you should interpret this in the Contractor's favour.