If the engineer truly just wants the bores to perpendicular to each other then a perp call out of one to the the other is correct. This way their relationship is not dependant on any other feature of the block. What you have described as being the call outs on the print do NOT amount to perpendicularity!!!!!
If, however, the engineer wants what you have described on the print then perpendicularity is not what is wanted. Perpendicularity is not dependant on a Datum feature but rather is a purely 3D description of the relationship between 2 features.