Adapt ``init_bold_reference_wf`` to use the new ``init_epi_reference_wf``

[oesteban]

The idea is to avoid most of the massaging happening inside the old pipeline, since the references generated with the new workflow (#610) are ready for masking/registration.

In particular, the N4 and 3dUnifize steps are not necessary anymore. In addition, we could consider dropping FSL BET completely, and use the new masking we are testing in SDCFlows (which would require upstreaming interfaces here).