Tbh I think perhaps you’re overthinking this a bit. In my mind projects are any tasks that have multiple sub tasks. So yes, I can absolutely envision a module as a project. But more importantly, I think by restricting yourself to specific semantics, you are really restricting how you can use JD. For example, for me 100-199 Personal is a collection of any items that are related to my personal life. One of the projects in it is 103 Wife stuff which contains any documents that I’m storing for my wife. Is it technically a project? No. But I’m not too hung up about that. The point is there is a way for me to organise my digital reference material and I’m happy with that.
If you haven’t already please give this page a read Multiple projects | Johnny•Decimal. Particularly the section, “How I name my files and folders “. It should explain why you should use PRO.AC.ID.
Lastly, I went for this format because I knew i will be working on more than 10 projects throughout my life. So the way it’s organised is 100-199 is personal stuff, 200-299 is research projects, 300-399 is teaching related stuff. Within research projects 200-209 are EU funded projects, 210-219 are RCUK funded projects and 220-239 will probably be research proposals.
If it helps you to organise your system as ARC.PR.ID instead of PRO.AC.ID then I see no harm in that. It’s achieving the same effect.