Is this possibly more of an issue with recognizing what each "storage unit" is useful for, and then organizing the usage of it? In other words, I see you saying that Workfront documents is kind of sucky because it can't do anything like OneNote, SharePoint or OneDrive... but... they can't do anything like each other, either, so I'm not sure there is a single solution.
On my own team, we do have a preference for using these same tools, so at the project level custom form, we have fields to link to each on a per-project basis, and then I have a view on a project report that shows me the project name, followed by the onedrive, one note, etc. links (I call it my reference library and it is a very specific solution that works BECAUSE we use these links for reference).
Other teams have utilized the Cloud Providers section in the setup area to be able to link sharepoint, dropbox, and other cloud drives directly into the Workfront documents section.
If you have Proof, I've also had reasonable luck or success with convincing people to put their sharepoint links into the Workfront documents folder by utilizing Interactive Proofs -- these convert that sharepoint link into a proof object which will live happily in the doc folder alongside your actual file uploads.
Anyway just two or three different options for solutions that have worked for three separate teams.
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