Perhaps the application is allowed to write to the %appdata% area even though the user can't. Have you tried doing this with a macro from within Word?
Code:
'Update the theme colours
With ActiveDocument.DocumentTheme
.ThemeColorScheme(msoThemeDark1).RGB = 0 'Black
.ThemeColorScheme(msoThemeLight1).RGB = RGB(255, 255, 255) 'White
.ThemeColorScheme(msoThemeDark2).RGB = RGB(61, 65, 70)
.ThemeColorScheme(msoThemeLight2).RGB = RGB(208, 211, 212)
.ThemeColorScheme(msoThemeAccent1).RGB = RGB(252, 76, 2)
.ThemeColorScheme(msoThemeAccent2).RGB = RGB(240, 179, 35)
.ThemeColorScheme(msoThemeAccent3).RGB = RGB(97, 94, 155)
.ThemeColorScheme(msoThemeAccent4).RGB = RGB(217, 192, 169)
.ThemeColorScheme(msoThemeAccent5).RGB = RGB(0, 178, 169)
.ThemeColorScheme(msoThemeAccent6).RGB = RGB(72, 159, 223)
.ThemeColorScheme(msoThemeHyperlink).RGB = RGB(1, 66, 106)
.ThemeColorScheme(msoThemeFollowedHyperlink).RGB = RGB(97, 94, 155)
.ThemeColorScheme.Save FileName:="MyColorTheme.xml" 'Overwrites if necessary
End With