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It's likely this is the problem:

<param name='robot_description' textfile="$(find sisko_mira_description)/urdf/r2d2.urdf.xacro"/>

A .xacro file is not a plain URDF, so it must be parsed by xacro before uploading it to the parameter server.

Your first .launch file treats it as a plain text file, so what gets uploaded to the parameter server is the raw contents of your r2d2.urdf.xacro, which is not a proper URDF.

Hence the complaints by RViz and the partial model (it does the best it can apparently).

Your second .launch file does this:

<param name="robot_description" command="$(find xacro)/xacro $(find sisko_mira_description)/urdf/r2d2.urdf.xacro"/>

Note how xacro is used here to parse your .xacro and then return the result. That result is valid URDF, so now consumers of that URDF will be able to parse it successfully.

As to the rest of what you describe: I don't know right now why RViz complains about missing transforms.

I would suggest you first fix the .launch file and then proceed with further debugging.