implications of difference between RMS and mean in rectified and non rectified graphs
My question is, would it make more sense to find the mean of the
  rectified graphs and the RMS of the non rectified graphs to compare.


The basic lack of understanding here is that you will find: -

RMS(unrectified) = RMS(rectified)

The squaring process (i.e. the "S" in "RMS") ensures that after squaring both waveforms are identical.

So, the RMS of a rectified signal is exactly the same as the RMS of an unrectified signal.

As a footnote, the average of a rectified signal does not equal the RMS of that signal.