Start and pushback clearance is requested from Ground or Tower, on receipt of that clearance then, depending on aircraft type and checklist, the before start checklist (probably already completed to a certain point), continues and the Beacon is switched on during this process to alert the groundcrew and anyone around the aircraft that the engine start process will commence imminently.
There are many cases where ATC cannot see an aircraft, it is not for that purpose although at smaller airports it may assist them.