You're looking at two different things, there. The example from Macro Initialization > Interactions > Highlight is specific to the Highlight macro (which is used to draw an additional 'highlight' around an area - Insert > Documentation Macro > Documentation Macro). It is used for the setting when that macro is first inserted. into the Project.
The example under Playback Settings > General is used for the 'highlight' for all interaction macros (such as Mouse Action or String Input). These settings should take effect at display time ("Playback") and not creation time so if you change it here, will be applied to existing simulations when they are played. If you are not seeing this (or your users aren't) make sure you have published your changes to the Playback Settings.
In terms of changing these settings in the Project (as Jesse mentions) - which you should only need to do by exception - for example, if you have a project recorded against an application that uses a color scheme that clashes with the default highlight color) then you need to do it in Tools > Settings > Playback Settings > General > Project Overrides > Highlights...
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