Yes, the dilution will lower the values. As to just how much will depend on the process, joint preparation, position, wall thickness, amperages used, etc. For example, very high energy processes, like SAW on a square butt joint can lead to high dilution levels, as can processes like GTAW on thin sheet.
Then you run into the fact that the dilution levels at the surface of a cap pass are often significantly lower than they are at the root or sidewall areas... add in two different base metals, and it's an even bigger bag of worms.
Can you give us some detail as to why you're running PMI on a weld deposit? Are you trying to verify whether the correct filler material was run on a joint, or is there some other reason?