For instance, when using a separate admin theme, NAB will pick up region options from the admin theme that is displaying when the cck type is edited, not from the active system theme (default non-admin theme).

Having a separate admin theme is common (if not a best practice), and the above behavior creates havoc with blocks on sites that are affected. Re-saving nodes, for instance, can cause their associated blocks to be disabled.

Similarly, if a per-node method of theme assignment were to be used, I suspect there would be a similar problem.

NAB thus should recognize the actual theme and display region options based on this, or, for instance, have a global "any region" option that avoids the issue.