Malloc and free have runtime overhead — sometimes more than the overhead of garbage collection.
The only way to have no overhead is to statically allocate fixed sized buffers for everything.
If I'm reading a file, then opening and closing a file is not overhead either. But if I'm reading a file and some convoluted system in my own process is slapping some 3000% extra work on top because it needs to asynchronously track opened files and close them at arbitrary time later - that is overhead and creates bugs.
Which is one reason why many GC languages end up with bad emulations of an almost overhead free pattern like "try-with-resources" in Java and "IDisposable" in C# etc.
I think you are assuming that a garbage collector calls malloc and free and then does a bunch of additional work on top of that to keep track of memory allocations, but that's not really how it works.