My observation is that untrained ears often hear intervals of something less than an octave (like fourths, fifths, and sixths) played in the lowest octave of the guitar range as muddy and indistinct.

This is not to say that this is the reason that guitar chords are diagramed as they are, I think that's mostly because the makers of chord charts want to simplify chords with the root as the lowest pitch.

The trouble with some open chords having four strings (like the D major is most often shown) and others having six strings (like E minor) is getting the same volume dynamics from strumming them. It's a good argument for playing D major 200232 so that a consistent range and dynamic is available...assuming that's what's wanted. There are other examples excluded here for the sake of brevity.

I also prefer certain barre chords, B minor for example, diagrammed 224432 with an F# as the lowest note rather than X24432 because few people seem to be able to consistently miss the sixth string. Adding an indeliberate low open E to a B minor chord sounds like crap...even worse with a Bbm.