No they will not be the same.
The encoder counts is what the encoder outputs in one revolution, for example if it is a 2500 line encoder then that would be 10,000 pulses per rev, if its a 2000 line encoder then it would be 8000 pulses per rev.
The steps per unit in Mach will be determined by the encoder pulses per rev, what gearing you have between motor and screw and what the pitch of the screw is.
For example if you have a 5mm pitch screw and the gearing is 2:1 between motor and screw and the encoder is 2500 line (10000 ppr) then the steps per unit would be
10000 x 2 /5 = 4000steps per mm
Hood