Anthropic's model deployments for Claude Code are likely optimized for Claude Code. I wouldn't be surprised if they had optimizations like sharing of system prompt KV-cache across users, or a speculative execution model specifically fine-tuned for the way Claude Code does tool calls.
When setting your token limits, their economics calculations likely assume that those optimizations are going to work. If you're using a different agent, you're basically underpaying for your tokens.