What do you define as "taking a loss"?
Not every game will be using the haptic trigger features and higher precision rumble of the dual sense, not every game will be using raytracing, or make use of the full IO effective bandwidth. I bet very few games will even use or require the USB port, and I bet very few people will make use of the M.2 SSD slot.
All of these cost money to implement, so you could interpret them as taking a hit.
New console designs are also based on how hard the console makers want to push new features. It's not just a bean-counter approach on how many people used the old features on the old consoles.
At some point they draw the line on what comes integrated and what doesn't. A 60GHz radio for better wireless VR headset integration apparently didn't cross that line, but it's not that obvious to me that it shouldn't have, especially considering we don't know prices for anything.