You can't control it to the level of individual LLM requests and orchestration of those. And that is very valuable, practically required, to build a tool like this. Otherwise, you just have a wrapper over another big program and can barely do anything interesting/useful to make it actually work better.
What can't you do exactly? You can send Claude arbitrary user prompts—with arbitrary custom system prompts—and get text back. You can then put those text responses into whatever larger system you want.