I manage a group that works on issues living in multiple JIRA projects. Version names are generally synchronized across all of these projects, however if I want to view a list of issues sorted by the Fix Version, JIRA will do a an implicit primary sort on Project Name because the Versions of the same name are actually different database entities across the different projects. Effectively, there is no way to sort on Fix Version across multiple projects in JIRA.

I would suggest adding new custom fields called "Affects Version Name", "Fix Version Name", and "Component Name". This would allow a user to sort their issues on these new columns which would not implicitly sort based on the Project first.