You shouldn't have picked air filter as your example.
Cars ECU's learn. They need to to pass emissions standards and meet performance figures.
They need to work correctly at a variety of altitudes (air pressure), air temperature and humidity. They also need to work when the air filter is full of dust.
The ECU only needs to know how much oxygen is going in to the engine. It will do this via one of two ways. manifold air pressure or an airflow meter. Both of which are not effected much by the air filter.
As for transmissions. Manual transmissions don't usually have computers. The speed sensor is simply a pulse per rev on the output shaft. Automatic transmissions are a completely different ballgame, a lot of modern cars have the transmission computer integrated into the engine computer. It makes it cheaper and much easier to control the selected gear and manage throttle during shifting, etc. As far as the physical transmission is concerned though, it's all mechanical parts. There's no problem pulling one out and replacing it with one of the same type.