For some reason, the format and version information and the dark module are not included in the mask optimization process. This changes the optimal mask in some QR codes.

However, according to the ISO/IEC 18004 from 2015 - 7.8.3.1 Evaluation of QR Code symbols:

Although the data masking operation is only performed on the encoding region of the symbol excluding the format information, the area to be evaluated is the complete symbol.

So I think they should be included.