That is a hard requirement to using Visual Studio and XCode, which I wager account for more than 90% of C/C++ projects.
Here's how my build system will do it: the programmer will list default build profiles. Then the build system will generate Visual Studio or XCode files that include all of those default build profiles, but those VS or XCode files will simply call my build system with the correct build profile.
Thus, when a build is run from VS or XCode, my build system is still in full control.
In essence, instead of generating build files for use by other build systems, my build system will generate files to tell VS and XCode how to call my build system. It will tell VS and XCode how to integrate it.
My build system will actually have a command-line option to reverse the dependency resolution. Instead of building a given target, updating its dependencies as necessary, it will build the default target(s), marking the files given on the command-line as "changed" and resolving dependents up to the default target(s).
This will mean that building the "current file" will be a simple command-line switch that can be part of the file generated for that IDE.
But yes, I'm going to put in a lot of work to make IDE's work as smoothly as possible.