I'm not sure if i understand well your suggestion. Do you want that:
a) User properties of source segments are propagated to the instances of RailClone Tools.
Currently, user properties are not preserved, but i think that would be easily fixable.
b) Create and assign new user properties in the style workflow, and export them in RailClone Tools.
For example, instead to change material ID, assign a user property with the color (or any other thing).
This is more complex, because RailClone has not any operator or mechanism to handle user properties/tags.
Is the Railclone tool utility able to be edited consumer side to help? The current ('Move to layer' is similar to moving to our desire to 'move a selection set')
No. RailClone Tool is written in C++, and integrated in the core of RailClone. It's not possible to customize it.
Anyway, if you need some specific feature which may be useful for other customers, we'll add it to the wishlist.