Nowadays I just install Xubuntu, add i3 and mostly use it as it is. So the terminal happens to be white on black and the Emacs black on white. I don't think about it, but apply the rule they give for healthier sitting: The next position is the healthiest one (meaning switch often).
I don't even know whether my terminal and my Emacs (main tools besides the browser) use the same font or not. Why would that interest me as long as I can read both? Sometimes when something has changed on a new installation (UI people want to do continuous improvement...) it might look ugly at first. After 3 days I don't notice it anymore. Hardly ever that I would spend any time to change it back as it has always been.
If you present online (other than slides) you should know the shortcuts to change the fontsize. And possibly change your cursor and selection color to make them recognizable for remote attendees.