Commerce shipping extra weight formula considers only base charge if order weight is lower or equal to minimum weight. It applies extra weight rate for any excess weight above minimum. Some greek shipping companies use this model of charging (i.e. ACS).

For example lets say we set these:
Base rate 5 euro
Minimum weight 3 kg
Extra weight rate 1 euro

If order is below 3 kg shipping will cost 5 euro
If order is 5 kg shipping will cost 5 euro + (5 kg - 2 kg) x 1 = 7 euro