The scalene triangle's application to bonsai comes directly from art - which means it comes directly from what humans typically find appealing, and the way humans recognize a shape or composition to be natural (and unnatural).
The asymmetrical scalene triangle is a "natural" shape. Symmetry (say, like an isosceles triangle) is almost never found in nature. Therefore, we humans tend to appreciate (on an unconscious level) the more natural form of the scalene.
This applies directly to composition as well. Three is the magic number in art - including bonsai art. Three-point display is not Japanese, it's merely effective artistry. Three elements in a bonsai display are most effectively composed in an asymmetrical arrangement. Other factors, like visual weight and center of gravity, determine how best to arrange the three elements with respect to the center of the display area.
The idea of heaven, earth, and man representing each of the three elements in a dislpay is concerned with the specific message communicated by the presentation and is helpful in culturally-specific relevance in some situations. However, it is not the basis for the 3-point composition. This sort of idea is applied to the already appropriate compositional form.
As you pointed out, the basic triangular form is also a commonly found formation for individual trees - natural so that all of the branches get sunlight. Narrow at the top and wide at the bottom is typical for a host of species. It is also typical for many other species at specific stages in their maturity. This form can suggest immaturity for many tree species, as they often end up taking on a more ovoid form in maturity.
This oval form also only works when the branch structure and foliage is more open and sparse, facilitating the survival of the shorter lower branches. Otherwise, they'd be shaded out and die off.
Anyway, hope this helps.