Project Management - Best Practices and tradeoffs

I am assuming you want to use MS Teams, if this is the case, you cannot  currently assign permissions to different channels (this is coming but we don't know when) this means that you have to use the Team as your security boundary.

 I would create a Team for each Project, this will give you a SharePoint site for the files and and Azure AD group to contain the people. Each user will be able to sync the Document Library to their local computer for offline work on a project by project basis, The OneDrive Sync client will expose those files in Windows explorer.