Because you want to have the thrusters fire into the ship so it can accelerate away from it, not try and alter the ship's attitude like a rcs.
I don't understand. The pattern shows rocket flames similar to what a cluster of four rockets at the stem of the putative mushroom would create, if the nozzles were aimed a bit outward - so the result would definitely be one of accelerating away from the ship.
again, when have we ever seen rocket burn marks in TOS?
Probably every time we saw a rocket. Which was, IIRC, never.
It's not as if future rockets would be "mark-less", though. We just never got a look at the marks Soran's rocket or Spock's boots would have left.