I bench bleed a new MC using short metal brake lines back to the reservoir. How do I prevent air getting back into the MC when I remove the short brake lines to install it into the car?

It's been a long time (decades) since I've done one, but if my recollection is correct, it's not really an issue. not much of the fluid drains out, and it's all below the piston/bore anyway. If you are going to flush the system at this point, well the air will come out of the caliper bleeders. If not, and the MC doesn't have bleeder screws, you can bleed it on the car by cracking the pipe unions one by one as a helper presses on the pedal. If you have a pressure bleeder (I've never used one), I suppose that would work in place of the helper. Vacuum bleeders are useless in this case. Obviously have copious rags under to keep the fluid off the fenderwell.