The behaviour is in fact expected, though it can be confusing due to the awkward naming of the "Alpha Is Transparency" option in the Texture Importer Inspector.

The 3x3 textures in the repro project have the "Alpha Is Transparency" option toggled on. This toggle tells the importer that any fully transparent pixel (alpha == 0) won't be visible at all. As such: the RGB values of pixels with alpha == 0 are modified/pre-filtered using an algorithm to prevent possible filtering artefacts.
(For clarity, this toggle actually does not modify the behaviour of texture transparency in shaders or such, currently it only does what I've described above! The preview in the inspector is unfortunately a bit misleading...)

Since the pixel in the middle of the 3x3 textures have alpha == 0 and "Alpha Is Transparency" is toggled on, the algorithm modifies the RGB values of these middle pixels. As the texture is very small, the result can seem a bit odd though it is the expected result of the algorithm.

In this case, in order to obtain the expected RGB value for fully transparent pixels, one can simply turn off "Alpha Is Transparency" to disable the pre-filtering that occurs while importing.