When an instance is part of a group and a smart:filter is either in group or track & group mode, the filter is adapted to reduce masking effects among group members. The special filter computed to perform this adaption is the “group filter” that can be seen when switching a smart:filter to group mode.
As potential level changes caused by the group filter are done on purpose to create a mixing hierarchy, the Auto Gain ignores its impact on the overall level. Otherwise, the group filter would reduce the overall level of a signal - and the Auto Gain would work against it by boosting the gain again.