The new errors (really they are considered "Lua Warnings" by the game) are there to let you know about a potential problem - and as mentioned above they are also not new, just went mostly ignored previously since they were only logged to FrameXML.log. And those errors usually point to a possible problem that might creep up on you down the line.
For this one specifically, you cannot reliable re-declare or version a XML template, so if it ever changes in a future library version, there is no guarantee of it working properly. So in short, avoid any XML content in embedded libraries, because there is no way to properly handle that - never has been, now the game just warns you about that more directly.
If someone really cared, you could probably make a dropdown-replacement library in pure Lua, instead of piling hacks on top of hacks.
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