I don't think that's true, there is plenty of people that are confident in max, pure data, reaktor etc or are a good at writing code but that never used a soldering iron in there live. For all those people axoloti could be an entry point to making there own hardware. And yes if you really wanna go that road you'll need to leardn soldering but I think the entrypoint should be as easy as possible.
In this discussion you should not forget also that people (including me) are lazy. I have a teensy at home but I never used it because there is an accumulation of little hurdles: You need to solder pin headers to both the board and the audio shield, then stack them together, then there you still have to write code to use it etc.
So again, make the entry point easy and then give possibilties to grow. This is what I see realized with the current design!
Axoloti on the contrary is plug and play, you can use it right out of the box and it works without seeing a single line of code. And I'm happy it will stay like that.
Yes pin headers are the best! BUT if you look into commercial products you might find an stm32. But you will never find it as an development board with thousands of little shields attached with ribbon cables.
You are much more likely to find the processor and components on one board, sometimes connectors and controll elements (displays, pots etc.) are on a second board. So if you wanna match the standart of professional hardware you will have to redesign everything anyway.
As a matter of fact I know hardware makers that use axoloti for prototyping but they would never use it in the final product, even if it was reduced board.
1. because of what I'm pointing out up here: you want as few pcbs as possible
2. you reduce your margin if you have to buy the brain of your system from someone else
This might be the perfect solution for you but not for everyone. Your "better" is just subjective depending on on your needs and preferences.
Where is your limit of "unpopulated"? It was already brought up here, even the teensy has a usb port and some people based on there needs and preferences might even want this port gone.
So no matter what choice you make, it is never the choice for everyone. Me personally I'm happy with this choice and I don't see so much how loosing a few mm of space for some mini jacks, that as pointed out here you can leave unsoldered is such a big issue.
EDIT: Of course I see that from a certain perspective, these couple of mm that you loose through unpopulated jacks can make a difference, but as I pointed out that is just one perspective.