Overall, you're right:  Tokyo is virtually a concrete jungle, with trees and greenery too few and far between.  Yet there are some ("ANY") examples, weak though they may be, of city-level efforts to inject some nature in the urban gray that you can't totally dismiss:

Yoyogi Park,

Meiji-jingu Garden

Shinjuku Garden,

and, to a lesser extent, Ueno Park.

And an aerial view of Tokyo shows that it is not altogether barren of greenery (click on "Satellite" to view the image more clearly.)

If I were going to mount a "religious/non-religious" theory of environmental relations, Japanese agnosticism is not what would inspire me.

Rather than, or perhaps in addition to, "agnostic", I would say "non-monotheistic" and "non-dogmatic".  There is plenty of "theism" in Japan, if only the polytheistic/animistic/pantheistic kind.

Truth unfolds in time through a communal process.