Even with a cost plus contract, certain variations should not increase the total price. A variation that amounts to purely a substitution of work should not result in a price increase. Neither party requested the variation. It just happened. The project changes course.
Nobody knows why.
The best safeguard against stealth variations is a well-written project plan. With a well-written project plan, there is no place to hide. Any deviation from the plan, any change in course, any mid course correction, will be self-evident. Most stealth variations occur when the parties take shortcuts. They do not prepare a detailed project plan.