Of note, the latest thing in reference genomes is representing them as a graph data structure, which importantly allows variation to be incorporated. Some of the newest methods for mapping short DNA fragments (that come out of the most common type of sequencers) take this approach. They use a genome index though, which takes a lot of computational effort to build before hand.

Anyway, benchling wants to avoid genome indexes from the sounds of it, in case users upload their own genomes. Having said that, if someone is doing multiple searches, it would quickly become more efficient to just index the genome. I would have thought most people seriously concerned about off target CRISPR hits would be using high quality reference genomes though.