Engine room and Atmospherics  changeup.

The supply pipe in Atmospherics no longer cross the middle of the room, after having seen many a complaint about this. Now passes through the aft windows instead.

Atmosphere technicians can now assist in handling the engine waste without entering the engine room itself.

Engine waste canisters are now pre-labeled according to future contents. Can be re-labeled should someone desire to try the oxygen setup instead.

The engine core now uses a similar setup as the atmospheric tanks, allowing control of the injection/extraction of gases from the monitor room.

Pipes  in the engine room overlapp less, making them easier to follow.

There is now a basic meteor protection layer around the engine room like solar panels have. Should stop a lone meteor or two, for anything more Renwick shields will still be desirable.
There is also a fairly wide gap by the ejection port, to ensure the supermatter doesn't snag into it, where meteor can sneak through.