You do not need to use the model alignment tool if you only migrate a single stream of models.
The model alignment tool only aligns models that retain the same overall structure. If you often refactor models in a later stream, you cannot align them. You must propogate any refactoring and partitioning into all related streams before you perform a model migration and alignment.
The model alignment tool runs in multiple stages: it creates a database of identifiers and then continuously updates the database. After a migration, you can align a hierarchy of successive generations of streams. For example, you can align an Enterprise stream with child streams that represent a line of business and projects.
You can also place the database of identifiers under source control, so that you can use it for subsequent migrations. When you align models that are under source control, you must also check out the initial set of migrated models that you use to create the identifier database, because the alignment tool also aligns their model elements.