I think that the waiter's purpose in the drama is to provide an outsider's point of view to the intense metaphysical condition that is ongoing between Andre and Wally.  In the end, both of them are engaged in a discussion about the nature of reality in which we, as the audience, are like the waiter.  We are on the periphery of this discussion, seeking to understand it in our own consciousness, but we are also challenged in terms of being able to either participate in it or do much about it.  The waiter is much in the same position, as it appears that he has an understanding of what is happening in the discussion and what might be at stake with it, but he also understands that his own capacity is not to be an active participant in the dialogue.  It is here where the waiter is marginalized, to an extent.  His only hope is that his voice will be validated by the implications of the discussion.  In this, the waiter's presence is one of an outsider, but also one who has relevance as to the discussion of both figures.  In this, the waiter is a figure that deals with the real world implications of the discussion, similar to the audience.