The engine computer is responsible for controlling the timing of the spark and the pulse width of the injectors to achieve an optimum fuel/air ratio.
It uses data from the MAF, Crank Sensor, Cam Sensor, BAP sensor CAT sensor, and others.
The MAF sensor tells the computer how much air is entering the engine. It uses this information to determine how much fuel to give each cylinder. If you change your MAF to allow more air to enter the engine, the new MAF either needs to be able to tell the engine computer the correct information translated to what your computer expects, or your computer has to learn to expect different information.
Pro-M and C&L mafs use slightly different ways to get the computer to accept the larger MAF without having to understand new parameters. Problem is, these tricks are not always optimum.
A chip fine tunes the system much tighter, giving the computer specific information related to the MAF signals it can now expect. This often helps clean up some odd idle behavior. But only if the odd idle is caused by the computer. If you have a vaccum leak before a chip, you'll still have one afterwards.