A SOM or System On Module provides a complete x86 type PC in a single building block. All the signals (HDMI, SATA, USB, RS232, LAN, LVDS etc) are routed via 1 or 2 bottom connectors. For development purposes a test carrier board is available. This development board routes all the above mentioned signals to standard USB, HDMI, LAN etc connectors.
A custom x86/PC based motherboard can be created by developing a custom carrier board. This is a rather complex process and should only be attempted by companies with access to PCB design capabilities (function can be outsourced).
With a custom carrier board unwanted features can be removed and non standard features can be added. In this way extra IO cards might be eliminated by adding the functionality to the carrier board. The carrier board can be made to be any size as needed.