After a discussion I had on IRC Freenode #ubuntu-unity I have now a solution which I wanted to share.
It is fairly easy to turn an ordinary scope into a master scope. To start just create a normal scope e.g. by following the scope tutorial.
The only thing which needs to be different is the scope file. Instead of copying it into a specific scope your directly copy it into /usr/share/unity/scopes/. Additionally in the scope file add IsMaster in the scope section
[Scope]
...
IsMaster=true
As a master scope can define its own filters and categories add those as needed to your scope file as well. Here an example I copied from the files.scope file:
[Category recent]
Name=Recent
Icon=/usr/share/icons/unity-icon-theme/places/svg/group-recent.svg
DedupField=uri
[Filter type]
Name=Type
Type=filter-checkoption
SortType=display-name
OptionIDs=documents;folders;images;audio;videos;presentations;other;
OptionNames=Documents;Folders;Images;Audio;Videos;Presentations;Other;
Per default won't your new master scope show up as an icon on the dash. If you want to do so you will need to change gsettings which you can do with the following command:
gsettings set com.canonical.Unity.Dash scopes "['home.scope', 'applications.scope', 'files.scope', 'video.scope', 'music.scope', 'photos.scope', 'social.scope', 'mynewmaster.scope']"
Replace mynewmaster.scope with the name of your scope. Done.