[Talking from the perspective of Eclipse, because it's the only IDE I invested my time in]
In this case, it's not. Eclipse put Integrated into IDE, but doesn't subtract transparency in the process. You can see what it does, tweak every step meticulously if you want, and return to defaults with one click, if you prefer.
What this transparency brings is mental flexibility and understanding. Do I want or need to switch? I'm doing the same thing in Vim or KATE of BBEdit in 15 minutes. Maybe I stumble with a couple of shortcuts, but that's not a problem.
The funny thing is I see the compiler command every time I press build, so it's burned in my memory after a day. While I can read valgrind outputs and understand what it says, Eclipse highlights the lines automatically, so I'm faster. While I can gnuplot performance graphs, Eclipse auto-builds them so they are on my desktop after a 10 hour torture run.
In my case, Eclipse enables me to carry a whole toolbox and more in a single folder, yet all the tools it uses and what it does is so transparent that I can switch away on an instant if I don't get my installation with me, or I'm connecting to a server in a datacenter far, far away.
I don't like to be blindsided by my tools. I like blinkenligths in a way, and Eclipse gives me these blinkenlights while being highly automatic.
So while I understand your case, it doesn't apply to Eclipse, at least, because it's not a strangler, but a great enabler and HUD in my experience.
For the time investing part, I don't grind. I get a tool, and start using it, and when it becomes limiting, I start poking it and learn what feature solves that problem at hand. By that way, I learn the tool as I go, and if the tool can't expand to my needs at some point, it fades away from use gracefully. I don't do "stop, drop, roll" thing while changing tools, so I can't paint a timeline about when I picked a tool and dropped another.