Yes the training will make them minimally stronger without significantly breaching large gaps in power such as the existing alphabetical ranking.
Cha intends to train to get that little bit stronger, or rather - as strong as feasibly possible. She's not training with the idea that she'll improve massively since that doesn't happen. She might re-awaken, but that has nothing to do with training and is a lottery.
I agree that the necromancer/must-obey thing is how this is supposed to work. That's how it's been shown thus far. Until Berus, essentially.Since those shadows are basically undead ghosts, Jinwoo being the necromancer, they are all his slaves, to put it bluntly. He should never have any trouble controlling them, regardless of what they thought of him while alive. However, we have already seen Iron do some stupid stunts as a shadow, just like he was stupid in life. The stunts are just somewhat different since as a necromancer's summon, he will be forever loyal and thus any disobedience won't play a role. That doesn't mean the shadows wouldn't do things on their own to varying degrees, probably dictated by the power level in life, which seems to lead to higher intelligence as a shadow. And any personality quirks.
And given that's how the command/summon is supposed to work, questions like "Don't you resent having to serve me?" or "Can you thin them out?" are meaningless.