I know you can replace the pipes in order to get the machine to retract it, but this way you can do things a bit more easily with automated systems.
Instead of having to remove the pipes, you can apply a redstone signal, which will put the pipes back in the slot and fill the hole with resources from the chest.
It means that the centre slot could be a dedicated mining pipe slot, and that if the miner is moved you can remove the signal to have it drill down again.
This would also work well with minerbased cobblegens too.
IMO, there isn't any real loss here, its fairly easy to implement, and a bit more intuitive, logical, and cleaner than removing the drill from the chest.