That thinking of making all your speakers as "small" when you have a sub depends on how much control you have over your sub and the sound you want your bass to have. When I let the Denon set it that way, I listened to how my Yamaha and my Denon set the dynamics, and said, "oh my god this Denon sucks!!! Let me send it back as quickly as possible." That is how they tell you setup to make things easier with having just average fronts. If you have spent thousands, in my case over $3500 for 2 front speakers, they were designed for performance WITHOUT a sub, as just stereo speakers, period. In those cases, you have to do a lot of tweaking about what frequencies and cutoffs you set for each speaker including the sub. My Focal towers have 4 front firing 6" speakers and one dedicated floor facing 6" speaker that will out perform any speaker I have owned or heard, even at over 100 Watts continuous, but pairing them in a 5.1+ system takes some adjustments and can be more tricky.
My $750 Klipsch R-115sw Sub does NOT do a better job at reproducing from about 90-200 Hz than my Focals do, but in fact makes the bass sound muddy when it's taking all of the bass from all of the other speakers, and it makes perfect sense. A one sub system has to reproduce bass from multiple sources (speakers) at once and "sum" them, meaning when the speaker cone should be going "out" with one low note, it is being forced to go back "in" early to reproduce another channels low notes at different times and different frequencies. Hence the reason if you have a room big enough, my Denon will play 4 separate subs, each dedicated to it's own channel, and doesn't have to worry about "summing" all the channels bass sounds. My room is not that big. So, in some instances, like mine, I get much crisper, punchier low end bass down to about 80 Hz out of my Focals, and let the sub do its job below that.
My only point and complaint about Audyssey is that it does a really terrible job at really listening to not only your space, but your current speakers in your system, where my old 14 year old Yamaha 7.1 Natural Sound AVR does it perfectly, and if it could play Atmos, I would have never replaced it. The Denon is the way I had to go, with a $2000 price ceiling, and it plays so many other codecs other than Atmos, but head to head, the Yamaha still sounds overall crisper, especially low end, yet smoother and more "Natural" sounding than digitized.