https://github.com/simtr/The-Powder-Toy/blob/6c725cc40588f505565f8939322e8b1983b16760/src/gui/game/GameModel.cpp#L302-L308

Easy way would be to add an if to the above snippet of code to skip adding the element to the tools menu for your specific tool and adding it yourself like the other tools just below. Removing your tool from sim->tools may have adverse effects on the code, I didn't study it thoroughly so you might see stuff like memory leaks or other kinds of glitches.