Currently the only way to include a color with a custom brush is under the New Tool Present button within the Tool Presets toolbar.
The implementation of this option does not seem very well thought out.
If you are saving a custom brush with a color this option should also be available under the New Brush option in Tool Properties.
After all you are creating a custom brush that has a specific color included.
If this were the only way to create a custom brush it would make more sense the way it is now.
When you offer a specific button for creating a specific tool you ought to include ALL the available options within that category.