But they don't tell you that if your data goes outside of their model, they will charge you thousands of dollars per hour to customize the "outlier" data.
I agree. Many of these apps are designed to meet 80% of client requirements. The other 20% requires customisation. Which is where I often make my money. Typically the 20% is required by only few users, and most clients are reluctant to spend a large sum for only a few users, even if the requirement is just below business critical. When this happens I can generally offer a solution based around Access/Excel for a fraction of the cost.