I think it's not surprising. I think for any psychoactive compound you are going to have some profile of brain activity that's triggered by that psychoactive. And it's also the nature of brain connectivity that if you repeatedly trigger a certain pattern of activity you will reinforce the corresponding connectivity. In other words each psychoactive triggers a particular circuit and the way the brain responds to triggering a circuit is by strengthening it. So using different psychoactives will strengthen different circuits in your brain and each psychoactive will have its own characteristic circuit, that gets strengthened the more you use it. In that sense it's really just like any other repeated activity. If you want to be cute you can consider psychoactives as some sort of exercise for your brain.

On the other side of that you can think of it as if you're focusing your brain activity on some particular circuits then other circuits will probably not be getting the same amount of balance detention but you would normally give them without the psychoactive. As a consequence of that their connectivity will decrease.

The study states that (at least from the abstract) coffee drinkers have lower connectivity in regions associated with sense impressions (smell, taste, touch, etc), emotional and memory processing and the unconscious. And higher connectivity in regions associated with visual processing and motor skills. I think this is not exactly straightforward to translate from that to what it actually means for a person's experience, because the connection between brain and personal experience is complex. But the way I interpreted it is if you drink a lot of coffee you probably going to spend more time twitching your body and intently watching your surroundings than you are ruminating about emotions and memories and various sense impressions. Based on the subjective effects of cofger that people report and how you can observe the behavior people drinking coffee, probably not a bad interpretation: big eyed like a lemur or tarsier and restlessly leaping all about the place, like a monkey...or doing the mental equivalent settled in their chair glued to their laptop.

but I suppose the crucial part of all this is that the connectivity affects do not just persist while the compound is in your bloodstream like the arousal effects do. the connectivity is like the tracks that the river carved out by flowing a particular way, so if you drink a lot of coffee I think what the study's saying is you're probably likely to spend more time focused on the outer world than you are on the inner experience and the connection to emotions, energies and so on.

As a another thing to all that: at the same time laying down circuits, or strengthening the existing ones, through repeated use is not the only thing that a psychoactive does. They have other effects, like he arousal effects of having caffeine in your blood, and side effects, and more. But even if carving out brain circuits was the only thing that psychoactives did, there might be some circuits your don't want to strengthen (like mice getting addicted to cocaine by strengthening its dopamine reward circuit, by pressing the lever repeatedly).