Most AVR's have to be made with cost cutting to all manner of components in order to pay the fees associated with all those stickers and logos on the outside of the box and keep pricing as low as they do. An integrated amp that doesn't have to pay for firmware, chips, ports and licenses associated with DTS, Atmos, HDMI, HDCP, Audyssey and so on. On an integrated amp the money (usually a higher amount) is spent on more robust toroidal transformers, circuits, wiring and other things related to improving sound quality. Less of them are sold (by orders of magnitude) so it's accepted by those who consider them that they cost "more per output watt."
When you refer to "integrated amps with only a "cutoff" of 100hz for the sub without a similar filter for the speakers is lame", are there examples of how this has tested to be true? I've heard Parasound Integrated and today the new Rotel RA-1592 and was very impressed that I noticed right away how nice they sound as compared to the Marantz SR5010 that was also demonstrated. It's not a HUGE difference, so one has to rationalize what value it is to oneself.