Third-party slice engines are missing from the Slice Engine menu
Third-party slice engines (Slic3r, CuraEngine) are available on desktop versions of MatterControl, except when using dual extrusion. In that case, MatterSlice is the only slice engine available. If MatterControl is configured with a dual extrusion printer the Slice Engine menu on the OPTIONS pane will not have either of the other slice engines available for use when using that profile.
If you want to print using only one extruder you could change the Extruder Count to 1 and select the slice engine you want.