None of the BEDTools functions require that a reference genome is specified. I don't even think that the "database" metadata for datasets needs to be specified. All of the genome content is self-referential, meaning that it is interpreted from the input dataset content itself.
If I did happen to miss a tool (or several!) that requires reference genome input - I would expect that either a custom genome or custom build could be used.
Please let us know if you need more help, Jen, Galaxy team