First, let state that I am not a structural engineer; but, based upon my time as a mechanical engineer overseeing construction projects I would suggest the following with the hope that more qualified forum members will lend more expertise to my comments.
The design thickness of an equipment pad is generally based upon providing adequate equipment loading support with a minimum amount of concrete volume and cost. So my first question is "who is paying the cost of the added concrete volume?".
Assuming the contractor is working under a fixed price bid and must absorb the added concrete cost, the good news is that the thickness is being added above the rebar level which effectively increases the vertical offset between the pad's horizontal center plane and the rebar layer plane and this increases the rebar structure's effectiveness in preventing tensile bending in the pad.
At the same time, the overall area of an equipment pad, in addition to being dependent upon the size of the structure, is also designed based upon the bearing strength and stability of the underlying soil; but, assuming that the equipment load being supported by the pad is significantly greater than the weight of the pad itself, the added pad weight may not be a issue.
Good Luck, in 14 years of onsite construction monitoring I fought many battles with contractors over variances from design specifications.