The contractor should not be the only party to pass the final test. It is like correcting your own exam paper. The commissioning of the engineer is then the exam to demonstrate how well the plant functions. Contractors think commissioning is like a structure. Once it is built you can walk away from it and it will live forever or at least for the next twelve months, the guarantee period.
Mechanical systems are different.
They are like living things with moving parts that can vibrate, make noise, burn out etc. So it is for the engineer to be ingenious and see their own original thought become reality. Unfortunately even the most idealistic engineer has to make a living and they have to be paid for their work. The engineer then specifies that the contractor must allow in the cost a demonstration of the system performing to the engineer's satisfaction. During the commissioning process the engineer even with the full knowledge of the design must become somehow detached and look at it unbiased and with no preconceived ideas.