Questions on SharePoint Online

Newlife, I'd recommend paring down your questions to be more manageable for someone to respond to--that's a huge list of questions with a lot of long answers, so I doubt you'll get much response with your question as is. Furthermore, some of these are things that can be easily tested yourself, such as OneDrive check-out, version deletion, major/minor versioning options, and discarding changes on file check-in; if you know to ask questions about those features, you're probably a few clicks away from getting those answers on your own.

I will share a few things on the more abstract questions:

• Enforcing naming conventions is difficult in any document management system. I would argue that if you require intelligence to your file naming, don't put that intelligence in the file name--put it in metadata and require that data to be filled out. SPO will let you upload documents without that metadata being completed, but it's not hard to identify what those items are (filters identify these quickly).
• You should have as many document libraries as you have specific audiences for documentation. Sites work best as containers for business units, projects, or systems, and your document libraries should take into account who should see what and whether or not the content of your document library has an overall theme. For example, I might have a site set up for a department with several document libraries--one of them might contain more sensitive documentation that only department leadership should view and modify, one of them might contain resources helpful to anyone in the department and anyone can contribute to, and one of them might be used for a specific purpose that maybe half the department actively works on but the other half needs to simply read. All of this is to say there isn't a strict "this is the best way to do document libraries" methodology--your document library structure should reflect what your business needs are and what your audiences need to be able to do and see.