Study in this area could shed light on (some of) the mechanisms of mental wellbeing: given that practitioners report that these states are extremely high valence, and generally useful to psychological wellbeing, perhaps they can advance research more generally into depression and other disorders/conditions. More specific to your points, if you want to do direct manipulation of the brain, how do you know what areas to manipulate? Studying the neural activity associated with Jhana could provide a target state for direct manipulation, rather than trying to figure out how to engineer good brain states from scratch or by analogy from, e.g. pleasurable drugs, which seem to have more side-effects like addictiveness.
Currently these states are not well-known, and given their association with mystical/spiritual worldviews, they seem to be dismissed as bullshit by many people that read about them (Citation: see the recent ACX posts). Objective research into the underlying mechanisms would legitimize these states (inasmuch as they objectively exist), and could lead to wider publicity and adoption amongst people with materialistic/non-spiritual worldviews. I view this as similar to how "mindfulness" has been secularized to provide beneficial treatments (MBSR etc.).
Related to 1, perhaps understanding these states better can allow us to do biofeedback to make them easier to attain, or otherwise find new mechanisms for teaching/inducing these states. (This one is a bit more speculative in my opinion).
Some ideas for why this research might matter: