‘ Therefore we said, “It shall be when they say so to us, or to our generations in time to come, that we shall say, ‘See the pattern of the altar of YHWH, which our fathers made, not for burnt offerings, nor for sacrifice. But it is a witness between us and you'.” '
Thus the presence of the altar, and the fact that it was patterned on the altar in the Tabernacle, which they could not have known had they not have been members of the covenant, would be evidence in the future of their part in YHWH and act as a witness of their religious rights. The fact that it was not used for burnt offerings or sacrifice would in fact emphasise that it was a symbol.