To accurately compare numbers, they must be computed on the same basis, using the same definitions.
If there are differences in methodology, you must recompute the numbers using the same methodology.
Non-comparable information is frequently provided by government. Definitions are changed for various political reasons. Often the methodology used for computation and comparison is obscured. Numbers are computed on different bases from year to year to "spin" the numbers. Comparing non-comparable numbers can be used to show that the economy is growing when it isn't, or certain groups of people need more (or less) government aid, or there aren't enough (or too many) teachers, etc.
However, there is simply no way to compare numbers computed using different definitions as a basis for the calculation. It is absolutely essential to compute numbers on the same basis before comparing them.