You're seriously contemplating a $1,000 machine, while being concerned about wasting a $10 stencil?!
Tons of fabs offer panelization. Heck, I don't think I even know of a fab, that would charge more than $1000 for an order, for a board that any bargain proto service (JLC) can fab. It's not even custom, it's just going to be standard proto stackup, right?
Tim