Usually contracts are never fair - ie. contracts are designed to protect their owner. This is almost always the case when it comes to a Contractor's agreement form.
What you can do to alleviate the headache is have your lawyer draft a simple "Custom Rider" to go along with the GC's agreement form. Basically, the "Custom Rider" states that the terms and conditions of the "Custom Rider" will supersede the terms of the Contractor's Agreement if ever a dispute does arise.
Let's hope your selection of contractor was good in the first place so that this does not happen.