As I said before, you need to re-evaluate your statement. It is filled with errors. When you can recognize those errors and correct them, then you will see that there is no exploit there.
"he has a crewmember enter the pilot's room and gain full bonus as if he were in the seat even though he's merely stepping into the room"
This is an error. He did not gain "full bonus." He gained a function piloting system since someone was in the room, and so he has full use of the engines, but no bonus from the pilot. The Stealth B starts with Level 2 engines, which gives 10% evasion. They are manned by an inexperienced crewmember, so the engines get a 5% bonus. Adding that 15% to the 60% provided by the cloak gives him 75% evasion, which is what you said he had.
"When I try that, the crewmember does apply unbonused piloting evasion to the room upon entering"
Same thing that happened with him. So you shouldn't be going around and saying, "This doesn't work on my version," when you already said it did. You are contradicting yourself because you made an erroneous statement.
Just to make myself clear, I think RNG plays a bigger role in failure than lack of skill. RNG has to give you stuff in order for your skill to become relevant. CE adds so much stuff, that it is harder for the RNG to bless a player. To me, that is the harsher environment of CE. I have no desire to ever play that. I just use CE as an occasional modding source. (Ship, ships with artillery for CE users, and a gameplay mod; a small plug of my mods that have been influenced by CE.)