I’m not sure if you’ve solved this issue or not, but we’ve had to come up with a solution for a similar situation – we have two screens side by side, also projecting through ProPresenter, and wanted to use Prezi – so if it helps, here’s what we came up with.
What I did, as the creator of the Prezis, was to set up each Prezi in a 16:9 aspect ratio, then create a transparent PNG file with black bars on the top and bottom, according to what our actual screen dimensions were (lots of trial-and-error to initially figure this out). I added some grid lines to the PNG image, for my own help in laying out each slide, then imported this image file onto each new slide (or copy and paste once it’s been imported initially). That way, I got to keep working within Prezi’s 16:9 parameters, but knew where to stay within the boundaries of where our screen would cut off the slide, top and bottom. (But don’t forget to delete this PNG image before saving the final Prezi – and be careful not to lose any of the slides on the path that may be attached to the PNG rather than the invisible frame!)
As for a workaround for ProPresenter, I just download the finished Prezi file (non-editable) onto a laptop, from which we run a video output cable straight to our software/hardware (Watchout, in our case) to send straight to the projectors, bypassing ProPresenter altogether. It works perfectly, once everything is set up.
Hope that helps! Best of luck to you.