Guys I have a question. Some of the assets are separate pngs (not part of a tileset). If I add any of these, Godot creates a whole new sprite2D for each. But if I do it this way, I'll end up with thousands of sprite2Ds, and my nodes will look very cluttered. I'm still a beginner, and the internet isn't helping
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which assets exactly are you talking about? Usually you want to create scenes and use the scenes in your world-node. Its not uncommon to have tons of nodes in your scene-tree, especially for worlds.
If you want a more organized approach you can create a scene-collection in your tileset and store scenes of your sprites in there. This allows you to place those scenes just like you would with tiles.
Such a question should be asked on the Godot Forum though