1. From the data sheet, section 4:
The device provides a combination of 1bit, 4bit, 8bit and 16bit ports, as well as wider ports that are fully or partially (gray) bonded out.
You can use pins X0D26..29 as sections of wider ports, but not all pins of those ports are available. For example, you can use X0D26 and X0D27 as bits 0 and 1 of the four bit port 4E.
2. The general rule is that, when pins are shared by different ports, the narrower port has priority. From the data sheet, section 6.3:
If a port is enabled, it overrules ports with higher widths that share the same pins. The pins on the wider port that are not shared remain available for use when the narrower port is enabled. Ports always operate at their specified width, even if they share pins with another port.
3. The audio platform uses the XE216-512-TQ128. Pins X0D08 and X0D09 are not connected, so in this sense they are wasted. However, you would be able to use these pins if the board allowed access to them.