How can placing a lone pair in axial position differs from that in equatorial in number of electron domains?
Here's a drawing of the situation.



In the example with the axial lone pair of electrons, when they say, "90 degree to three other electron domains", they just mean that the axial lone pair is situated 90° relative to 3 other substituent bonds - the 3 equatorial substituent bonds in this case.  When the lone pair is located in an equatorial position, then it has a 90° interaction with only 2 other bonds - the 2 axial substituent bonds in this case; the lone pair is 120° away from the 2 other equatorial substituents.