Legit question! The SD card and both USB pins are on header pins and in Euro I'll put all three accessible on the Frontpanel. It would be animal abuse to not allow an Axoloti instant programming.
Unfortunately the C-shaped header pins placement is quite fixed by now. This is so that there is enough space for a reasonable pot and button layout on the planned frontend board(s), and that is also why the USB jacks and SD slot are at the top. There is quite some circuitry for power management around the USBs.
At first I planned to leave out all connectors on the core board but felt it'd be much better if you had a minimal functionality where you could plug the core in as it is and get started (btw the recent revision has pads for a 3.5mm headphone jack squeezed onto the PCB bottom)