thirdhatt summarized it all very well.
the companion way give you a lot of privacy, i guess not a big concern if you live alone but when you have kids or guests, it's great compared to most smaller boats where the master opens directly into the saloon.
the 53 MY and 58 YF also have great ventilation thanks to the side doors, windows and the doors onto the aft deck. even in summer, at anchor, there is enough breeze coming to avoid running the AC. when i leave the dock, i like to be outside, not locked in with the air...
also, the side doors by the helm make it easier to single hand the boat which i do all the time as your spring lines are just a few steps away. once that's set you all... set
if you have to go down from a flybridge or back out and around like on the 58TC, it takes longer and gets tricky on windy ways.
i dont' think the 9' make a big difference, except for dockage and bottom paint. either boat will have 2 engines, gensets, running gear, electgricla system, air con pump, water pump... difference maybe one fewer AC and slightly smaller engines.
beware of what you "hear"... yes the two stroke DD are a little old now but pafrts are available and they are simple. all these baots came with them and even though some have been repowered with other engines, the DD are just fine... unless you're a speed freak...