Simple answer is to ask the estate agent as he is the best one to give the correct reason.
You dont need a licence unless you are being given a licence to occupy for a period of time prior to the start of the lease and this is a separate document. In some instances, if a landlord is prepared to give a rent free period but doesn t want it to affect the averaging out of the rental value they will give a licence to occupy untill you have fitted out or whatever then charge full rent for the rest of the duration of the lease. EG instead of 1 month rent free on a 12 month lease = 11 months rent, they give a licence for 1 month, then give a lease for 12 months at full rent. This means when investors or surveyors are analysing the rental values, they only see the 12 months at the full rent. This is the only circumstance in which the letting agant may be charging you for both. Hope this helps.
Ask them - we rent a number of commercial premises and have never done that, but serious industry might be different.