There are some addons (e.g. denali-mailer) that do some custom build behavior of the app they are installed to. Currently (unless I skimmed too quickly), there is not a way to do that. The denali-build.js returns an extension of Builder, so it shouldn't be too difficult to standardize a way of adding configuration that addons can then check.
Note: I'm drawing this idea from Ember's ability to pass in configuration to addons via the ember-cli-build.js file.