I haven't used the vise on mine much, but if the Atlas shaper vise has too much overhang, I'm pretty sure the Atlas milling vise will too. I think the vise part is the same on both -- just the swivel base that is different.
When I've had to get the workpiece close to the spindle, I've clamped an angle plate to the milling table and then clamped my workpiece to that.
Do have a plain (slabbing) cutter that you could use on an arbor with the support arm?