With proper fixturing it would not be an issue to do one end at a time. Even drilling the stepped hole in two opertions Using a forstner bit first for the big hole then a regular bit for the small hole. I would start with a long "V" block to hold the piece of wood that is to be drilled. If you have a floor standing drill press you could turn the table 90 degrees, attach your fixture and drill away. Getting the table to 90 degrees would be a fairly simple matter with a dial indicator. My time spent in a factory as a machine setup,QC and a little tool & die taught me a lot about fixturing.
Ken
EDIT: I would make the sides of the "V" block wide enough to give support to the engine side of the piece of wood being drilled. Not the skinny support you have pictured. With my setup I would mark the wood so the same corner always is against the fixture.
Ken
EDIT: I would make the sides of the "V" block wide enough to give support to the engine side of the piece of wood being drilled. Not the skinny support you have pictured. With my setup I would mark the wood so the same corner always is against the fixture.