A problem with this type of GUI is that they usually are centered
around a limited set of commercial applications: it works well as
long one stays within that limited scope, but one is left out in the
cold if one steps outside.
For example, the use of a "make" file gives full programming control,
that the type of IDE you mention does not.
If the GUI outputs a Bison parser, you can then build it under the
control of make. You could think of this kind of interface as an
alternate editor for .y files.