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Basically, your mount is aligned when the centre line of the polar axis is pointing to the SCP. The drive will rotate the scope about this point whilst tracking. Even if the mount is not level when setup initially, drift aligning will essentially compensate for this error during the process. The closer the tripod is to level and closer to south it is at the start, the less manipulation the drift alignment will need to adjust for.
I used to have a CG5 mount, the index marks I think are to give you a similar amount of movement on either side and it basically "centres the gears" if you like. Ultimately it shouldn't affect your alignment, but you may run out of movement if you were trying to look at something very close to the horizon...not sure on this though...I never actually tried it.
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