I wasn't aware such micro-sd extenders exist. But I expect one issue, the sdcard holder has a little switch that is used to detect card insertion/removal in firmware. The card will be mounted on startup without switch, but no hotswapping cards...
What's wrong with sideways mounting Axoloti Core (with DIN and power section cut off)? That 'd give you access to sdcard, usb host+device ports, bootloader switch, status leds. The jacks are probably of less use, but can easily be modded into nice extra's like footswitch or expression pedal input... Or removed to save a bit space, the MIDI part could be sandwich-mounted upside-down, the mounting holes align...
Clarifying my motivation for mentioning this: if the eurorack power supply uses a linear regulator from the 12V line to produce +5V, it will get very hot when a USB device is connected to the host port that pulls 500mA, as it will dissipate 3.5 Watt. The usb host port will still have a stmps2141 to protect against over-current.