Toe overlap has nothing to do with how the bike fits you unless you have your cleats waaaay out of adjustment. It is the geometry and design of the bike. Besides, how much of the time are you doing tight turns?

Your statement about the brakes is confusing. You can reach the brakes from the hoods but not from where else? Do you have extra levers on aero bars? Perhaps being a tri-bike, the bars should be that low. Are your aero bars clip-on and sit above the bar so he might have the bar set low on purpose?

Do you mean the stem is too long?

Tri-bikes don't fit like road bikes at all. They're weird beasts.