I just check, the way I think it works is this:
The color of the TW User has higher priority than the color of the IFC Model Change. This latter is actually the color of the Mark-Up Style. When IFC Compare feature is used ArchiCAD imports the changes and assigns various Mark-UP Styles to these elements.
So basically it is a question of which one has higher priority in display: TW User color or Mark-Up Style.
As I see TW User color has higher priority so when you are using a Colored Workspace Option in the Teamwork Palette it will color those elements marked up by the IFC compare feature.
But this should not be a problem because when you are using a TW Palette colored workspace option, the color of all elements is overridden based on TW User Color and WE settings, so you don't see what color they would have because of the IFC Mark-Uping.
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