Is it permissible for me to take a commission from my employer if I mediate to increase his profit through personal effort, by requesting it through an intermediary for fear of refusal or a small amount?

We understand from the question that you found a project for a second company owned by the same person who owns the company you work for, and you fear he might not agree to give you a suitable commission if you ask him for it in exchange for guiding him to the project and mediating it. There is no harm in appointing someone else for this matter, and you are not obliged to inform him that you were the one who guided him to the project, unless that is part of your official work for the company. In that case, such a stratagem is not permissible for you.