it's the ability to serve business customers who are 
    willing to pay for heavy customizations and the extra
    support those entail

You'd need to have flags in the app itself, which would likely turn into an unmaintainable monstrosity. If you have a handful of large clients, are heavily customizing the app for each one, are using a modern framework like Django or Rails and a DVCS, the obvious maintainable approach is to have full individual installs, forks for each install and a modular application that pushes the customizations into pluggable components as much as possible.