Thank you very much, that helped me a lot!
I have found and corrected the issue. The problem was, that there appears to be a bug with the custom post type filters. While it was set to invisible, it still was in effect, causing the problem. I have reset the post type filters to default, as it is not in use. I will of course make sure to fix this in the upcoming release.
Now it should very likely display variable results based on variable SKU-s. I hope this helps!