I think a better comparison would be to look at the HBP numbers exclusively in a Red Sox-Yankee vacuum.
Because I can guarantee that 75% or more of Jeter's 12 HBP's have come against Boston this year.
Here is your vacuum!
Head to Head Pitching Comparisons (2007) New York VS Boston
Games -- Yankees (14) Red Sox (14) W -- Yankees (7) Red Sox (7) L -- Yankees (7) Red Sox (7) S -- Yankees (4) Red Sox (4) IP -- Yankees (122) Red Sox (121) ERA -- Yankees (5.61) Red Sox (5.43) H -- Yankees (145) Red Sox (135) R -- Yankees (79) Red Sox (75) ER -- Yankees (76) Red Sox (75) HR -- Yankees (21) Red Sox (18) BB -- Yankees (68) Red Sox (59) IBB -- Yankees (5) Red Sox (0) SO -- Yankees (75) Red Sox (86) HBP -- Yankees (7) Red Sox (7)