In the end that depends on the mod you are using, but you are right, I asked Rothgar to implement the custom file for exactly the reason that I wanted mods to be able to function without those files.
You know how for some new windows you always needed to edit eg the eq2ui_mainhud.xml to add an <include> line or two until an updated version of your mod was available. If mod authors now use the new eq2ui_custom.xml instead that means you will never have to manually add <includes> again when SOE updates the UI.
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