It grew from a direct parody of the old cliché about Playboy magazine - "I only read it for the articles (and not the naked women)". The corresponding phrase is "I only watch My Little Pony for the plot (and not because of anything sappy or girly)". "Plot" has thus come to have connotations of salacious content linked to female nudity (although approximately M-rated as opposed to X-rated). As the MLP character designs don't tend to have even the suggestion of breasts, but can't exactly avoid having butts without their hind legs falling off, "plot" in an MLP context therefore become linked to the concept of pony butt in a rather convoluted way.
It is not etymologically linked to the phrase "plot of land", or even "huge tracts of land".