I use one (1) extra series column -- called "subseries". For story arcs e.g. Riftwar, Legend of Drizzt, etc. (the main series column gets the universe series order).
I don't really have any crossovers.
When it comes to anthologies, you will just drive yourself crazy. Use the EpubSplit plugin and divide the anthologies into individual per-story ebooks.
You might be able to get away with
NO custom columns.
I certainly don't see the need for more than one extra.