For mITX fit would really be a case-by-case (hah!) basis, since the board is a bunch wider than the 17cm of mITX. (m)ATX with 244mm it'll much more likely fit (I think few cases really strictly limit to the 244mm). That'd mean you can have one side of ports positioned at the port bracket.
In either case ports on the other side would be good to expose, and for many port types you can get extension cables that end in a panel mount which could be placed in the I/O bracket or in a slot cover.
If the (from a laptop-user perspective) left side is exposed:
Outward-facing are Power, Ethernet, Audio, SD card. Ethernet and Audio are good to have there, SD card is IMHO "meh" (doesn't hurt to be reachable, would also be ok to be hidden in the case). If Power is needed to connect to the PSU it's not a good place and would need a cable snake out and back in immediately, which is possible but ugly. If the PSU powers the board through an internal connector just plug the Power hole to make sure nobody accidentially connects a PSU. HDMI and all USB ports are internal then - in combination with a GPU HDMI isn't needed, if a user wants a different card they'd need an extension. Some USB ports also could be sent to front-USB ports, but some USB at the back is probably preferred by some - if so that needs an extension.
PCIe port is on the side pointing towards usual GPU position, so to install a GPU there the riser connecting it can be very short but needs to bend back 180°.
If the right side is exposed, I'd want Ethernet to be extended to the back. Audio in many cases could be sent to a front port. Power is fine internal, SD card is fine internal. Back has USB ports and HDMI. Front-USB could still be fed from internal USB ports (i.e. the trackball one).
PCIe port is on the side pointing away from the usual GPU position, so a riser would go straight across the MB and then to a card slot.
For a custom case I imagine mainboard and and GPU back-to-back, which would give you something about as wide as a Reform, 2-3x as thick and probably shorter in the third dimension (depending on power circuitry exactly), so that the ports are exposed as they are in the laptop? That'd work quite well to mount it behind a screen (VESA mount?), or to have it with USB ports to the front and GPU exhaust to the back on a desk. HDMI at front would be a bit odd, but also not needed if used with a GPU (and could be behind a stylish cover)
All email clients support HTML message bodies