Theoretically you could have more control if you started at the ROM level. You could remove the ROM board (if that model has it on a removable board) and then you make a new board with an adequate EEPROM or something easy to work with. You could start from absolute square 1 with this approach in 68k ASM. You could even have your own custom startup sound this way if you so choose. By default there will be no startup sound until you "recreate" it.

If you get a chip large enough, you can make your whole OS right there onto the ROM, and it would be LIGHTNING fast. This would be a huge undertaking, though, to say the absolute least. I guess this approach is similar to making ROM cartridges for Commodore 64. You could easily skip the whole OS concept and program an application directly that will be running immediately when the machine is switched on.

If you connected some sort of external connector and made cartridges, the original ROM could go in a cart for normal Mac functionality, and you could make all separate carts for all your neat ideas and experiments that you could easily swap out. This would be an ideal way of getting those technical details you're looking for. Unhindered experimentation is possible, and really I don't think you could hurt anything this way except maybe your self-esteem after a while.