The difference is the lens system.
Lenses are not made for that focal, they are made for the original focal length.
You can crop the sensor as much as you want but you are using only the equivalent part of a lens system that was design for a different focal length. A lens system for a 100mm is different from one for a 200mm.
And yes, if you use a perfectly equivalent sensor with its own lens system (made for that focal) it will be better than the cropped version from the bigger one.
There is a reason why photography brands rarely do this and when they do it is always to be able to use a different format lens (that was made for that sensor size).
A full frame camera could have this feature to use aps-c lenses but not to just "magnify" the full frame ones.
Once you "start" from the same sensor and lens system, cropping the sensor only has a small advantage compared to just cropping a photo.