You are correct, the OS itself usually only runs up to about 80G.
Where people have the trouble is that they forget to change where they save things like documents, downloads, and other media while running their smaller boot drive. As a rule of thumb you don't want to go over 90% use of an SSD drive or it starts slowing down drastically, so ideally you won't fill your 120GB past around the 100GB point.
It is certainly do-able to have a 120GB boot drive, and many Tom's users here have one. You'll just need to keep an eye on it a bit more than if you were able to get the 250GB drive.