Yes, it does have to pull fuel from the main tank. In essence, the header/hopper tank gets filled from the main tank.

However the result of adding the header is that the engine is mainly only drawing fuel from the small tank (closer). As far as the engine is concerned, that is the level (distance) of the fuel tank. Another benifit is its drawing fuel (sucking) through a much shorter run of fuel tubing. Long fuel tube runs on a 'suck' system can be tricky. The header/hopper tank helps reduce the long run and distant tank effects. Also, the header tank tends to stay absolutely full most of the flight, keeping the clunk "wet" all the time.. no chance to grab an air bubble.

Yes, there are liquid levels/head pressure and stuff involved. Its not a perfect system. But it works.

You will see many of the helicopter pilots flying with a similar arrangment, for similar reasons. The fuel supply is effectively closer to the engine, and there is less chance of sucking air into the pickup line.