In the color palettes the colors always follow the order Light 1, Dark 1, Light 2, Dark 2. As it is frequent practice to put dark text on a light background the colors are labelled Background 1, Text 1, Background 2, Text 2.

As you noted this is not the same order as in the Customize Colors dialog. Not that it matters as these colors can all be used for either text or backgrounds.

By default, Word will use Dark 1 for text. If you look at the VBA enumeration wdThemeColorIndex you will see that this is referred to as wdThemeColorText1.

In PowerPoint, the first four colors are used as the default background color options. Word doesn't automatically apply background colors as the "background" is the color of paper being used.

The images to the right of the dialog show the colors in use to help you judge whether there is sufficient contrast between the light and dark colors. It also shows the accent colors applied to a bar chart to again judge the contrast.

As all of the colors are labelled the fact that they appear in a different order in the color palettes is of no importance.