You cannot seal the ECU. The best you could do is know where it is located so you know how deep you can go.

On a Nissan Sentra the ECU sits on the hump on the floor before the center console so you'd need to have water up the handbrakes to fry it. On a gas-powered Pajero, the ECU is on behind the glovebox (high and dry), on most Isuzus the ECU is in the engine compartment (be careful), on a Fortuner it is under the driver's seat.

The dipstick is reasonably sealed (check if your dipstick has a gasket). And more often than not, the dipstick opening is about the level of the tires already. The breather can be extended using rubber hoses. Off-roaders have been doing it for years. For a manual transmission with the shifter directly entering the transmission body, there is really no practical way to seal that entry point.

Stock air intake systems will have safeguards against water ingestion. Just know where the intake draws air from (some draw beside the headlight, in the wheelwell, from the bumper etc.). At least you'll have an idea how deep the vehicle can go.