The metatags for a page manager page variant appear to be added to a page twice, once from metatag_page_manager_metatags_alter() and then again in metatag_page_manager_page_attachments().
An additional issue with this, and what caused me to discover it, is that this means you can't override any metatags by implementing hook_metatags_alter() or hook_metatags_attachments_alter() in your own module. This is because the call to metatag_page_manager_page_attachments() is happening after those hooks are triggered in the main metatag module, and then not triggered again. Currently, if you wanted to override the metatags of a page manager variant, you'd have to implement hook_page_attachments() and then override things there, defeating the purpose of the metatag module hooks.
I believe the solution here is just to remove metatag_page_manager_page_attachments(). Reviewing the metatag_views module, it only has an implementation of hook_metatags_alter() to add its metatags. I've bypassed metatag_page_manager_page_attachments() in my custom module via hook_module_implements_alter() and everything is now working as expected.
Needs review
2.0
Integration with other module
Here's a patch that just removes metatag_page_manager_page_attachments()
Thanks for reporting the bug and for working out the fix.