I don’t think letting IDE edit the build system automatically is a good idea, In visual studio there is XML based build system that is not human editable and to edit build parameters you should go into several windows and tool options instead of writing single line and then after some releases they might change tool option location and because of that many learning resources turned to be unusable in few years (worst of all vs compiler doesn’t have CLI at all).
in my opinion IDE way is not good for building stable and software and It will adds layers of complexity and unnecessary abstractions because they always try generalize and I don’t see any IDE can solve this issue not Anjuta, builder, VS, netbeans, eclipse, or inteliji.
although autotools comes with his problems but dependency of perl is more stable than python and autotools is mature.
since you are good at autotools I can’t recommend anything new to you but for any beginners reading this thread I recommend the following resources: