Most flexible manufacturing systems come with a central tool storage (1000+ tools) that can load each individual machine's magazine (usually less than 64 tools per machine). The solution to the problem you mention is adding one more non-humanoid machine. The only difference is that this new machine won't consume the tools and instead just swaps the inserts.

There is literally no point in having a humanoid here. The primary reason you'd want a human here is that hiring a human to swap tools is extremely cost effective since they don't actually need to have any knowledge of operating the machines and just need to be trained on that one particular task.