I use containers to separate system context (partitioning cookies and site data) while remaining in the same user context (e.g. "personal browsing").
I use profiles for when I need different user contexts (different bookmarks and frequently used sites for different clients or projects).
When only one tool is available, you are limited by the constraints of that tool (e.g. bookmarks bleeding over between user contexts when using containers, or having to copy extensions or bookmarks into every profile).