The short answer is "No, the PM does not have the flexibility apply the funds inconsistent with how their use was detailed in the approriation."

The appropriation bill is Congress's plan and is so directed to be followed by the President after he signs it into law.

I will assume that the AAP is asking about a mark based on the real-time markup of the FY23 appropriation. If the FY23 appn comes out with line adjustments as detailed in the question, the program office may have no choice but to reduce quantity (regardless of the quantities cited in the NDAA) to buy only fully useable end item to comply with the full funding policy, while complying with the level of detail in the law. Disregarding the language of the appn puts the program at risk of willfully violating the Purpose statute.