We did have the pump on the OY rebuilt back around 1995. And yes it did go in and out through the hatch in the roof. I got the air to work correctly on the OY too. OY has the old A1 system with a G6 valve, plain triples under the Rotary and tank, etc. We never had it work before because somebody had taken the rotary valve out of the brake valve in the pilot house. As we didn;t have any other A1/G6 stuff, we cut it out and let the other engine have the air. There is a straight air independent brake on the OY and tender long with a trainline dump valve to stop things if necessary.
Anyway, we rebuilt the pump, got the air to work, using parts from 463's old A1 equipment that we changed to 6ET. I was a proud and happy guy. 5 minutes before blast off from Chama, the OY's pump makes a big BANG and starts running fast. It turns out the contractor who rebuilt it forgot to to cotter key the nut on the bottom of the piston rod holding the air piston on. The nut fell off and landed sideways on the bottom head. The piston and rod on its next downward stroke hit the sideway nut and punched it neatly through the bottom head.
We cut all the air out, and did a repair on the road heading toward Lobato. We stole the bottom head off OM (the only other one lung 11" pump on the RR). We got it all back together, but it seems, I left the automatic air cut out.
To quote one of my predecessors: "I love a challange, it's a struggle a can't stand".