Why does the BET equation take into consideration a multimolecular-layer, even though it deals with chemisorption?
Brunauer–Emmett–Teller (BET) explains the physical adsorption of gas molecules on a solid surface, and doesn't address chemisorption. Even the wikipedia link that you provided, makes that quite explicit. However, you are correct to think that it is in a extension of the Langmuir adsorption model, which only accounts for monolayers. 

The assumption that underscore this model are as follows:


  
  Adsorptions occur only on well-defined sites of the sample surface (one per molecule)
  The only molecular interaction considered is the following one: a molecule can act as a single adsorption site for a molecule of the upper layer.
  The uppermost molecule layer is in equilibrium with the gas phase, i.e. similar molecule adsorption and desorption rates.
  The desorption is a kinetically-limited process, i.e. a heat of adsorption must be provided:
  
  
  these phenomenon are homogeneous, i.e. same heat of adsorption for a given molecule layer.
  it is E1 for the first layer, i.e. the heat of adsorption at the solid sample surface
  the other layers are assumed similar and can be represented as condensed species, i.e. liquid state. Hence, the heat of adsorption is EL is equal to the heat of liquefaction.
  
  At the saturation pressure, the molecule layer number tends to infinity (i.e. equivalent to the sample being surrounded by a liquid phase)
  


References: The original article

P.S: Good reading material on BET theory can be found here