To run a custom action for a specific feature you need include the feature action state value in the condition logic.
<Custom Action="MyAction" After="InstallFiles">(NOT Installed) AND (&MyFeature=3)</Custom>
The & in front of the feature name will return the feature's action state. Possible action states are:
So to only run a custom action for a particular feature we check that it's action state is set to INSTALLSTATE_LOCAL which is 3.
MSDN - Conditional Statement Syntax
MSDN - Examples of Conditional Statement Syntax
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