Sort of.  In ALR calculations using PWM controllers, all amp-hour losses are lumped together under system losses.  5% is a typical coulombic loss for a battery, so the coulombic efficiency would be 95%.  Another 5% is to account for mismatch, soiling, etc. so the total losses are 10%. In the MPPT model, the average charge voltage of the battery and the voltage drop between battery and array are also factored in. The charge controller efficiency is figured separately.