Yeah, sorry for giving you misunderstanding.
You are very true to say that small polygons less than certain amount should definitely dealt with, either removed as you have mentioned or aggregated.
However, considering importance of the small features from geological point of view, some small portion of polygons little less than threshold, considered for enlargement. Thus, once I got some of the polygons enlarged, the other constraint is violated, which is distance between polygons are less than it should be.
For topology, yes polygons are moved, but considering scale and the moving amount they are unnoticeable, as any generalized map surely has to some extent abstraction which lead to different type of errors.
Again, here we have to choose between aggregation (if the polygons of the same or similar category) and displacement.
So, making long story short, some portion of polygons are considered for enlargement to make them visible, as they may have important value to the geologist.
Thanks for your answer.