That's an important point.

Whether it's tools, MCP or skills: they are fundamentally all just prompts. Even if the LLM is trained to recognize those and produce the right shape of tokens that validate most of the time.

But I wouldn't use the word "understand" here, because that builds the wrong intuition. I think a more useful term would be "get guided by" or "get nudged by". Even "recognize" is slightly misleading, because it implies too much.