Hi @matt.curcio.ri!
It's not the most obvious thing in the world
, but you can sort the Files pane by "type" by clicking the empty column heading above the little file type icons:

This puts all the folders either at the top or at the bottom of the list. Does that match how your native file navigator sorts? I know that close-but-not-quite can be even more confusing when you're jumping back and forth between different views of the same filesystem!
If there are refinements you'd like to submit as a feature request, here's your starting point
:
RStudio IDE Guide: Writing Good Feature Requests. There was some discussion of this a while back on the old support site, but I couldn't find a related issue on Github.