I am in the process of creating a centralized database at work. Most of the information will be standalone but there are things that will have move than one file type. I know about libraries and lists and the dangers of folders. I also know that this is mostly doable with managed metadata but I want to compress my things into one thing- I know this doesn't make much sense and it may not be doable. My question is, is it possible to create a "book" or "folder" for lack of a better word that would comprise of a single project that has Word docs, PDFs, OneNote Notebooks, etc? I basically want to create a folder that has all of the project info in it without creating a folder in my database.
It sounds like you're looking for the Document Sets feature.
This allows you to bundle like documents together into a single "set" which can have additional metadata applied. A document set is essentially a special type of folder that supports metadata.
As long as you don't use folders in tandem with document sets, you should still be able to avoid the problems that arise from using folders in SharePoint.
The following instructions show how to enable and configure document sets for a site: https://support.office.com/en-us/article/Create-and-configure-a-new-Document-Set-content-type-9DB6D6DC-C23A-4DCD-A359-3E4BBBC47FC1