yes they do. factory units typically don't have the same type of attentuation for the emphasis for bass. We had a guy who had a factory cadillac unit and we kept on thinking it was his subs or amp that were the problem. He said he wasn't getting enough bass. We finally convinced him to change out the HU and it made a world of difference.
some mosfets, butterworth, and chebychev filiters will also be the SH!T too... After takin entire classes just on filters, YES it matters!! And it reflexs into the price tags as well!