For some reason the ggplotly call overrides most, but not all of my theme elements. It ends up overriding the legend in specific, which is frustrating considering that I always alter the position and justification thereof. Furthermore, in this specific case I use two geom_line() to specify a second aes for a second vector of my dataframe and use scale_colour_distinct to specify the line types and add the second vector to the legend.
Lastly, while the plot renders correctly in viewer mode when I specify the margin sizes, it does not respect the margin when it renders in a markdown document. In specific it continues to cut off the y-axis label nor does it observe my axis tick element settings in my theme function