The quality of the story is a matter of opinion, but the linearity of the story is objective fact. Just look at the chart you posted: there is one linear story to follow, with just occasional branches to alternate endings or splits that immediately merge back together.

Most VNs are structured as routes. There are a handful of independent stories. The reader not choose how the story will unfold, but rather chooses one of several linear stories to follow. I would classify that as a fundamentally linear story. The fact that the route is chosen by a choice in the middle is not really different from choosing the route from a menu at the start.

SubaHibi is even more linear than that, because the playing order of the routes is enforced. There is one "True" ending, which is required to be completed last and is the only one which resolves all the mysteries.

(I say the True ending resolves all the mysteries, but the mysteries were resolved to my satisfaction by the end of It's my Own Invention. That wasn't by design, though.)