Myself, I find this concept appalling, as my policy with customers, be they individuals, designers, or contractors, is that if there is a mistake and it is my mistake, I eat it. If there is a mistake that is not mine, or a change to be made after construction, then someone else pays. This is determined before any additional work is done.
My change order states the work that will be performed, that travel will be charged at x per mile, labor will be charged at x per hour, and materials will be charged at raw cost plus x percentage. After the change order is signed, the work is performed and an itemized bill with copies of receipts is sent to the customer. Time and materials is fair to all involved.
When people ask in advance about change orders, I have said that I have a credit card, a stopwatch, and an odometer all set to zero, and they will pay all costs incurred.
That you were not informed of the situation, much less not given an opportunity to make good on it, certainly violates contracting protocol. It sounds like the GC is making you the scapegoat in the eyes of the homeowner while the GC is trying to gouge the homeowner, and your reputation may suffer as a result. Also, the homeowner may file a small claim against you if the GC lays the blame for all of this on you.
If you have any rapport with the homeowner, tell them that you feel this charge is excessive, and see if you or they can get an itemized bill from the GC. If the GC signed off on the shop drawings, and signed as having received the cabinetry as specified and in good condition, then he may be on the hook for the change. This may require arbitration, and it will be necessary to determine who is at fault, who authorized the additional work, what the incurred costs are and who is responsible for those costs.
An itemized bill will shine some facts on this situation. Remember, what one person sees as embellished billable hours another person sees as fraud.
And yes, you should do your own installations, so that situations similar to this in the future can be addressed before the fact, rather than after.
Good luck.
TonyF