Hi NightCabbage, it's normal for the shaded filled area to be a giant sheet in the background - the shaded areas are done as a background bitmap those parts are not vector objects.

I tested the PDF export with Affinity Designer and Adobe Illustrator and in both cases a square and a rounded corner square do not come in as individual pieces, they are one curve each. So that seems to be a problem with Inkscape's PDF importer.

SVG output would contain just the same stuff as the PDF export so I'm not sure if it would improve anything for you. I guess maybe it could avoid the curves coming in as individual segments problem if that is a flaw only in their PDF importer.

Maybe if you file a bug report with Inkscape they could improve the PDF importer to behave as other drawing programs do instead of separating everything into individual pieces.

- Michael