I am reading the sections of the official documentation that talk about the feature and experimenting in Animate Pro 3, which in most cases functions like Harmony when the two share a feature.
The paint tool is mentioned several times when describing the feature however upon digging deeper I need to amend what I stated previously:
An important key I just realized is that the Protect Color and Respect Protected Color features work when there is a form of filling taking place. This feature protects the filled color. An enclosed shape can be filled with a color but a line made with either the brush or the pencil is filled with a color as well. Protect Color does work with drawing tools and their Tool Properties box even has a button to turn it off and on.
Protect Color only protects the filling of an existing line or enclosed shape. This does not prevent you from adding a line over the filling using an unprotected color. However, you cannot fill an enclosed shape drawn over a protected color. IOW, you can draw lines over a protected color and create an enclosed shape over a protected color using an unprotected color but that enclosed shape cannot be filled.
I suspect this last characteristic has to do with the way the software reads painted and unpainted areas. The new line is an independent object being created as you make the stroke but there does not seem to be any data generated that indicates and understands there is a separate enclosed shape made with the line. Once the stroke is complete the software only understands the line. The space inside the enclosed shape is not interpreted as part of the line object. It only sees the the area as space and therefore the protected color beneath it.
The documentation does not explain the logic used to determine why Toon Boon decided a tool would work a certain way. I cannot think of a reason why the software would deliberately prevent filling the new shape over the protected color. There could be a good reason. It may be an oversight.
Tutorials may elaborate listing a couple of situations where you might want to use a tool or procedure. The feature is suggested in the documentation when inking art. What would you like to use it for? How is it not meeting the task?