You'd tolerance the holes with position to only one datum (this is what Kenat was saying) and also use the MMC modifier in there. It doesn't control the median perpendicularity or anything like that. It would just control each hole to be perpendicular to datum A, but at the same time control their location from each other.
Then, when you want to reference back to that datum (of two or more features of size), you'd probably want to modify the datum reference with "M". See the attached graphic for an example from the Y14.5 standard; notice that the two small holes create datum B, but first they are positioned to each other -- and also to datum A (thus the perpendicularity aspect).
John-Paul Belanger
Certified Sr. GD&T Professional
Geometric Learning Systems