The better practice is, if it isn't a one-off, being introduced to the tool (perhaps by an LLM) and then just running the tool yourself with structured inputs when it is appropriate. I think the 2015 era novice coding habit of copying a blob of twenty shell scripts off of stack overflow and blindly running them in your terminal (while also not good for obvious reasons) was better than that essentially happening but you not being able to watch and potentially learn what those commands were.
I do think that if the agents can successfully resolve these tasks in a code execution environment, it can likely come up with better parametrized solutions with structured I/O - assuming these are workflows we want to run over and over again.