I managed to add my Unbreakable Lockpicks RootTemplate to my Enhanced Skillbook RootTemplate folder and saw the new lockpick in an existing save from earlier, so it's possible to merge mods that modify the RootTemplates.
That being said, while it might be easy now due to there being just two/three mods that change a RootTemplate, this limited mod issue will become more prominent in the future as more people make mods. This doesn't even go into the potential issues that item-adding mods might cause when merged (and/or removed); right now we can only really say that merging works for modifications of existing items/characters.
