The guidance on this page applies for the tax years up to and including 2015 to 2016. For tax years 2016 to 2017 onwards, the benchmark scale rates have been revised and are now included within the exemption for amounts which would otherwise be deductible. See EIM30200 onwards.
Many employers pay or reimburse, at scale rates, expenses incurred by employees in performing their duties. Subsistence payments are a common example.