We will call for the contractor to cast anchor bolts in a thick equipment pad with a tin can around the top of each bolt. The can will provide a void form for the concrete with the bolt located in the center of the void. The bottom of the bolt is anchored in the initial concrete equipment pad placement. The can is removed after the concrete cures.
Then the equipment is attached to the anchor bolts using leveling nuts. The voids allow some lateral movement of the anchor bolts to facilitate the proper location to match the holes in the equipment base.
Once the equipment is installed and leveled, nonshrink grout will be packed in the voids and under the equipment base plate.
I am not certain how this would work with chemical anchors or if this is even the same type of job.