This isn't clipping which is what that FAQ entry addresses. The Auto EQ appears to compensate for this anyway - when boosting on band, every other band is cut a little, presumably to keep the average at 0.

What I think is happening here is that the high dB gain pulls up the boost curve such that there is a positive boost extending below 1Hz, ie to DC. If you look at figure 4 halfway down this page, perhaps you'll understand what I mean. At low boosts (green line), the boost extends less than at high boost (blue line).