For where you're actually providing the dependency, I'd use
checkinstall to do the installation.
checkinstall basically replaces
make install and generates a proper .deb package and then installs that. Not only does that allow you to remove or upgrade the package in a better way (when the time comes), it satisfies dependencies from other applications.
The alternative is writing a little dummy package that doesn't provide any files but claims to provide whatever you want. The easiest way I can see is using an application called
sudo apt-get install equivs
# edit your fake package so it has the right versions, names, description, etc
sudo dpkg -i lilypond-dummy*.deb
There's a third route that is easy but the potentially harmful: just install it from the standard repos and then replace its files with the ones you generate. Lock the version of the package so it won't get upgraded. This has the scope to go wrong so only do it if you can't
checkinstall or otherwise fake the package first.