It's actually about context management. Calling a MCP tool will load a potentially huge json on your context window, maybe triggering a compaction. Using a subagent for that is less bad, but still expensive (and you wouldn't run every tool call on a subagent)

But if you had a mcp client cli, you can just pipe it to jq or whatever and extract what you need. or chain multiple tool calls into a single one. None of this will make the agent receive the intermediate text passed between those (the agent might want to save the intermediate results into temporary files however)

But shell scripting sucks. Javascript or Python is better suited for handling json and things like that. That's what is being called codemode.

Ok so.. it makes a lot of sense to integrate agents and programming languages. But right now, harnesses are more or less interchangeable and you can hop to another one very quickly. The more coupling between all those moving parts, the hard will lock-in hit. (just picture the mess that is Claude Code having a severe lock in on the ecosystem)