There is no such thing as "modelling in a file". I am simplifying a bit, but you could think of it like this: When you author building models, you effectively manipulate computer memory. When you save it, you write it to disk, often to a file. It becomes clear that there are two models (and their meta models) involved - the transient model in memory and the persistent model on disk. Import and export is the conversion between the two.
We can rephrase the question to ask why not use the same meta model for both, e.g. the IFC schema as the domain model of a CAD application. The answer to that is simple: CAD application data models are optimized along the criteria of the specific application, efficient display, navigation, manipulation, memory-consumption etc. While IFC has been design to cover many of the common principles and geometry kernels used in CAD software, it's purpose is data exchange.
Thus unless your application is exclusively about processing IFC files (storage, querying, analysis, comparison etc.) - and even then - you will need some other data structures to efficiently implement the task at hand. And thus you will need some mapping between different data models.