Studio versions are a work of art. They're a product. There's sounds that are used to present a certain atmosphere, setting, or to describe a sort of feeling for the listener. Whatever the song is about, the musician will try their best to present that product in their recordings.
If you watch Peter Orullians The Astonishing track-by-track, he relates these sounds and sound/instrument choices to provide more atmosphere, scene setting, and tone to the listener.
What I found with The Astonishing and the crying of Lord Nefaryus is that those are genuine cries. Crying is very similar to Laughter, in one makes you cry tears of sadness and one you cru tears of joy. Both can sound similar and I have heard many people cry where they sound like they're laughing. So I was not put off by that.
Now we go into the vocals and why singers or musicians choose to go for these harder sections in the studio, because that's what the song calls for. It's a reason to be aware of your fellow musicians and vocalists capabilities. Which is where the creative differences excuse comes into play where musicians leave bands, which this reason is they're not capable of doing what the songwriter needs for the song. Which then leads to solo albums or other projects.
Charlie was not capable of doing these high notes, which Dream Theater songs call for. It's why I find it sort of odd that they went with Dominici, and makes me think they just went with what they could at the time to keep that momentum consistent.
Then you get a great vocalist and then later on decide to write music that this vocalist is not capable of doing consistently. Pushing him to the limits live, expecting him to be perfectly in tune live is a pretty complicated and harsh expectation, if you ask me.