I understand the motivation for this approach. Custom development has fallen out of favor, and more "out of the box" features reduces time, cost, and risk for an implementation. This approach is not sophisticated enough to lead to the best choice, however.
Many features required in a line of business solution are inherently "custom" because organizations follow business rules and workflows that are quite specific for their industry and niche. Companies strive to differentiate themselves from one another, and therefore one size cannot fit all. Government agencies must conform to laws and regulations that are almost always more complex than an outsider would expect.
If you count all features as equal when scoring a proposal, you cannot capture the cost or effort required for customizations because the number of features that are separately enumerated is arbitrary to begin with.
Finally, clients often enjoy features that have been customized just for them. They feel more ownership of a solution when they are consulted on requirements, and when the user experience is tailored to their needs.
The real question is not how to avoid or minimize customization, but rather how can you find a system that supports customizations as painlessly as possible.