As I see this, there are two concerns:
1) Compliance with the Code
2) Compliance with your WPS
Looking at item 1 first: Unless you are working on a component within the Jurisdictional Boundary of the State you are working in or where the component will be installed, the code (any part of it) may be overruled by the owner. (Note - excluded from my comments is any reference to work involving the nuclear industry.)
Generally, the hierarchy of controlling documents (listed somewhere in the contract technical clarifications) lists the precedence. It will typically say something like, if a disparity between the code of construction and these specifications is identified, the contract specifications shall be followed. It's their right to make that call, but you should point the situation out. This could be an error on the part of the engineer and they may change it if it is pointed out to them.
Item 2: The requirements for filler metal classification / F & A numbers must be adhered to in accordance with your qualified WPS. If the component is within the Jurisdictional Boundary (ASME Section I: Boiler Proper or Boiler External Piping; or ASME Section VIII: Pressure Vessel), you have to comply with the code. This may require that you qualify an "unassigned" filler metal specifically for the application (ie - base metal welded with a filler metal that does not conform to the F or A number rules of Section IX.
I hope I haven't confused the issue. It's clear to me, but I know things don't come out the way we think them sometimes.
Charles.
Portable PMI instruments are usually used to check materials before they are installed to make sure a mix-up has not occurred, to check already installed materials to confirm them prior to welding, to check minimum specified chemistry for cladding, or similar applications. They are usually not accurate enough to verify conformance to a material specification, although some types are very good, so a plus or minus would be appropriate in that application. I would not consider this "overriding" the material spec, just recognizing the limitations of in-situ measurement methods. If compliance to a material spec is being checked, then laboratory testing methods are required.