So the question I have is the same as the one I found online but that's the only time I see it asked online. As it states, is there a way to change Sublime so that it displays files first in the sidebar?
It's still not currently possible to manipulate the display order of items in the side bar, with the exception of changing the order in which top-level folders appear if you have opened more than one folder.
It has been requested to add something akin to indent guides in the side bar in order to make it more visually distinct and clear where items line up, though. As of the current time, that has not been done.
In the interim there's not much you can do about this except to note that files that are contained in folders are visually indented, so in cases (such as in the image above) where a file and a folder have icons that line up with each other, that's an indication that they're siblings in part of the same folder structure and not parent/child. This isn't always helpful in all cases, though.