Because layer height of first printed layer is "your layer height" + "z gap parameter in Support / Object interface setting" + "Printer/Hardware/Bed Roughness parameter"
For the second layer it is just "your layer height" + "z gap parameter in Support / Object interface setting"
If You do not want gap between raft and object, You have to set Z Gap to zero.
If You want to use raft and also support, well You'd have to find compromise between object/support gap and raft/object gap. Unfortunately it is controlled by one parameter.