I can’t seem to find any official documentation saying that the Graph API removes the per-folder file count limits, though there is a user in List large folder in Onedrive for business (od4b) · Issue #2580 · duplicati/duplicati · GitHub who reported that the new backend worked around the error for them. Additionally, I was just able to create a folder with 20000 items, and the Graph API started paging through them without problems (I’ve been manually paging through, so I haven’t reached 5000 yet, but it seems to be working).
As for fixing this for the old backend, I don’t think it’s possible, as it was a limit built in to the old OneDrive SDK / API, which is being disabled in November anyway.