As of now, FileImporter blocks files that are not marked with a license that is allowed on Commons. However, in some cases it's still legally fine to transfer such files to Commons – after individual review and then marking them with the appropriate license. Logos are mentioned as an example.
What currently blocks this workflow is the fact the source wiki does not have a compatible license template. It only exists on Commons, and can only be added during or after the file was transfered.
The main open question, among others, is: How to make sure an "individual review" really happened, and not every incompatible file is moved to Commons? Can this be solved by checking the license after the user had a chance to edit the file description page? Do we need another config for licenses (the ones that only exist on the target wiki) to do this? Basically, this proposed workflow needs a proper UX design, to not mess with the currently designed workflow.