It is normal for a prefab shower pan drain to require an oversized hole around the pipe to provide clearance for the drain. So yes, if the concrete is poured up tight to the pipe, it will need to be cut/chipped/broken out so the drain body fits under the shower pan. If you are lucky, the concrete around the stub is not very thick.
If the drain is 2", it wouldn't really matter what it was originally roughed in for. 2" is the minimum size that should ever be installed under a slab.
You didn't mention anything about a plumbing vent, which is required. Depending on how things are layed out, the 2" pipe you are looking at could very well be the vent connection for the water closet, or the entire bath group.