The unifying abstract concept is that a certain amount of difference allows for some known factor of compensation or interference.
For example, an area of excess metal may be left because it is needed to complete subsequent machining.
If there was no gap between the axle and the bearing then there would be a lot of friction and it would be difficult to get the car to move.
The engineer designing the machine knows that in reality, the grinding operation that produces the final diameter may introduce a certain small-but-unavoidable amount of random error.
To be sure that there will be enough clearance between the shaft and its hole, taking account of the tolerance, an allowance is intentionally introduced in the dimensions specified.