Two problems, Jon ...
1. acs-reference was changed to be part of the core in 5.0, which is why initial-install was set true. Your changes apparently set it back to false. Dependency checking during the bootstrap install process is weak and this error wasn't caught. It would be nice if it were, but in practice the core set of packages changes very infrequently and the web ui level APM dependency checking works perfectly well so I'm not going to worry about it at this point.
2. You can't automount core packages with the *info automount property at the moment. acs-install.sql needs to run first, but that's not done until the basic install is complete (need acs-subsite to be installed first). We could *probably* get rid of acs-install and handle it via a "after-install" apm Tcl callback in acs-subsite itself, and with dependency ordering this would mean acs-subsite would be available when core packages with UI like acs-reference are installed. I'll file a bug report for 5.2 and assign it to myself ... for now we'll just tell people they need to mount it if they want to interact with data via the acs-reference UI. Rrankly I doubt many here know it has a UI so I think we can live with this until the underlying acs-subsite mount/install issue is resolved.
I've committed my changes and HEAD now installs ...
