The main issue here is one of UI. If you click a link in a PDF, what profile should the link be opened in? My take is that if you have multiple firefox instances it should ask you, otherwise it should just open on the only one open.
For example, one of the major use cases for this sort of separation is being able to use multiple accounts on a site like Twitter or Facebook (which don't support multi-account) or Gmail (which does, but it's a bit rough). There's no reason I should have to have separate windows or separate addons for each of those accounts.
The choice of container is no more or no less complicated than the choice of profile for links in external programs (or within Firefox)
I.e., Containers do NOT protect against some lower-level privacy vulnerabilities like plugin enumeration or history-sniffing that are mitigated more by using entirely separate profiles.