Apparent Meaning (Exoteric):
The proper place of Malkuth is at the feet, but to reach there we must stoop and bend down. This disturbs our grace and may cancel the affirmative divine energies imparted through the rite by making the student self-conscious. To those with physical difficulties it may also be impossible to reach the feet, or dangerous to bend in such a manner. On a final note, pointing to the heart puts us in communion with our Christian fellows, who utilise an alternate form of this rite (the Sign of the Cross [and the doxology of the Pater Noster or Our Father]). Thus, for mostly practical reasons, we draw the line of energy down from Kether to Malkuth, but point to Tiphareth for the latter while imagining the energy extending downwards.
Spiritual or Mystical Reference (Esoteric):
Malkuth is located at the feet, while Tiphareth is located at the heart. There is an intricate connection between these two Sephiroth, for Tiphareth is commonly known as both the King (Melek) and the Bridgegroom (Katan), while Malkuth is the Kingdom (its literal translation), and also the Queen (Malkah) and the Bride (Kallah). It will not take the student long to see that these are pairs, that they must be coupled, but there is an even bigger Qabalistic mystery at play: the Tiqqun, which is the Repairing of the World. For Malkuth is seen as fallen - it is the "pendulum" Sephirah on the Tree of Life, often depicted in older diagrams of the Tree with only a single path leading to it (from Yesod). It is the goal of the Qabalist, in order to enact the Tiqqun, to raise up Malkuth, to reunite it with Tiphareth, the Kingdom with the King, the Queen with the King, the Bride with the Bridegroom.
In the Qabalistic Cross we enact this Qabalistic mystery by pointing to Tiphareth when we vibrate "Malkuth", and this accomplishes two ends: 1) we affirm our goal to raise up Malkuth by intimating its position at Tiphareth (united with that sphere); and 2) we accomplish this goal on a smaller level (As Above, So Below) by energetically lifting up our personal sphere of Malkuth via the channel opened in this rite. In as much as we draw energy downwards, invoking the Divine, we also, paradoxically, draw energy upwards, transmuting the dross of the physical into that divinity.