I understand your concern. I doubt that you'd have to worry about breaking your transducer bracket by lowering your transducer to where it needs to be.
I don't know what material is used to make the bracket but I'm sure it can handle some abuse. I would move, modify or add on to your transducer mount if you really feel that it needs it to provide the additional support. Remember a little extra effort up front will pay dividends in your enjoyment for years to come.
Good luck with your install, you're almost there.