With off the shelf systems, you are essentially purchasing a piece of software used by thousands, possibly millions of people. The cost of this software is carried by the number of users- generally the more people using the software, the less expensive it will be.
With configurable software, you are purchasing the software plus the configuration services required to enable the software to function in your unique environment. This means that
a) The implementer needs to understand your unique environment
b) The implementer needs to understand how to configure the software
A high level of skills is required to do this, so the cost is inevitably high. The more skilled the implementers, the greater the cost, but the better the outcome. As a rule of thumb, even the smallest business will require about 100 hours of consulting services to work through this process. Multiply that by the professional’s rate/hour and this will give you an indication of why these systems are expensive to implement.