Agile's methodlogy now requires Continuous Integration, which leads to a need for these DatabaseProjects to be built on a headless machine, like a build machine.

Neither Studio nor Fusion seems to support compiling DatabaseProjects from the command-line. Whether it's a TFS agent or something like Jenkins, there is no opportunity for a UI-based tool to perform a task like this.

I suggest one of two paths:
a) Create a separate command-line executable that will compile these projects
b) Translate the DatabaseProject schema to MSBUILD schema (and/or schema of others' choosing, like ANT) so that it can be processed natively by the build environment

Since Fusion is specifically a Visual Studio plugin, it seems fair to demand that the custom database projects that come with it be in Visual Studio's MSBUILD language.

Without some way to invoke DatabsaeProjects builds automatically, this product is dead in the water under Agile and CI.