This really all depends on the coder. I work on a very large commercial project written in C++/Qt and Tcl. The majority of the main programmers use Emacs and Eclipse. I use qtcreator and vim. IDEs don't get in the way of project specific tools at all - that is why you tell it where all your bespoke classes and tools are. Most all IDEs understand Git, Subverison and Perforce as well as project trees.
The reason I love the IDE I use is the ability to quickly follow inheritance back to parent classes from some class or function definition, quickly find all uses of some function in the project tree, and just overall ability to hop around, switch from header to source, etc. Qtcreator even has vim mode, so all the easy text editing I'm used to is right there. I'm sure some programmers have scripts that do these things, or some Emacs/Vim magic, but I don't know it, and don't have the time or desire to learn it.
In the end, no one gives two shits what you use as long as you're productive.