The embedded object may be a SVG, IDK, but to the end user there is no “original svg” available (not in the versions I have available, at least). Assuming that the OP uses a fairly recent version of OneNote, the concept of “save to file” is not applicable. The notebook content is inherently saved in the “Microsoft ecosystem” (locally or to OneDrive, but not visible as a file) upon entry.
Also, I find that I can’t copy graphics from OneNote and paste into “foreign” apps like LO Draw. I can paste into other MS apps, and copy the pasted objects for subsequent pasting into LO. The overlap artifacts then disappear.
This supports your suspicion that the issue is caused by some Microsoft internals, which other PDF-supporting apps treat differently. I guess that doesn’t help much, but just in case: attached is a Draw file with my scribble intermediately pasted into MS Word, and copied from there.
copypastetwice.odg (49.0 KB)