Difference between Mini-ITX and thin Mini-ITX

There's an older version of the spec that's available at Intel.com: Thin Mini-ITX spec 1.2. The fundamental differences are:

1. Z-height restrictions on the I/O shield.
2. SODIMM instead of traditional UDIMM memory
3. On-board power-supply adapter, so you use an external brick power supply.
4. Locked CPU location. Many chassis have custom thermal solutions, so a locked CPU location still enables choice of motherboard.
5. Zoned I/O ports. This is more difficult to explain but due to the space constraints of an AIO, the wires can't have too much slack. Again, most USB ports, case fans, etc. are only deployed into certain zones to ensure interoperability between any chassis.
6. LVDS and some eDP support. Enables internal video. If your system has an integrated panel (AIO), you don't have to run a cable out of the board back into the panel.

Intel created this form factor, primarily aimed at being used in All-In-One PCs.

The easiest explanation is that they are thinner than regular Mini-ITX boards. Single stack ports on the back (I/O Shield height), (lay-flat) notebook-style memory sockets, etc.

Thin Mini-ITX desktop boards have a lower z-height to support more compact All-in-One PC designs.

Source

More info:

• http://www.intel.com/content/www/us/en/hardware-developers/aio-thin-mini-itx-desktop.html
• http://www.intel.com/content/www/us/en/hardware-developers/thin-mini-itx-desktop-boards.html