Many jobs don't match the plans (I might even say most) perfectly. We must then determine if the differences are significant. If a plan calls for a wall to be 10'5" from the exterior wall and it is 10'7" it does not match the plans. It is up to the inspector to determine if it is significant, and if they can't make that determination, or they believe it is significant then a plan revision and further examination.
I would note a few things with this project.
1) The owner did not approve the changes, this is a red flag.
2) The builder says it was to hide the HVAC. Hmmm, revise the HVAC? create a chase maybe?, but move a pantry without owner consultation?
3) There is a beam that appears to be questionably supported, it doesn't look like it lines up with the bearing walls (based on the "layouts", which are apparently the framing plans. That beam will deflect, and if you put a partition under it, it will pick up load. That load will cause the wall to deform (as others have noted), and any slab without bearing design could cause further stress via slab movement.
In this case I would be investigating more and would require a revised plan.