Regarding the colour issue, it appears the custom themes added in Start8 1.3 are not automatically picking up on changes to the colour scheme unless you change a Start8 setting.  This will be resolved in the next update, thanks for letting us know.

The other shortcuts are actual physical shortcuts in the OS which is why Start8 continues to show them, however I will see if we can add them to a list to make them invisible.  This will not be the default for the store and computer settings however as these are links that customers may need to access regardless of their desire not to see Modern UI apps.