I hear you. At some point someone is going to ask, “We’re paying how much for M365? And we’re not using it? Why?” But until you get a good training program to wean people away from what they learned on Windows 95, I know it can be a difficult task.
Search works in the Teams Client if you’re using it. We had an Epicor Team which held all of our Document Attachments, upgrade testing, work instructions, and conversations about ERP issues. It was great because new users could see the conversations held before they held their position and get up to speed quicker.
Since Epicor has a similar product in DocStar, I really can’t imagine them putting effort into SharePoint until it can be done throughout all Document Management. So…
If you really, really, really want to have subfolders, I think the price for familiarity is going to be having to upload the document to SharePoint in the subfolder created manually and then manually create a Link in Epicor using the LINK Document Type. 
Mark W.