First, as you have pointed out, question #1 is irrelevant, since you cannot choose GL_BGRA for your pixel transfer format in OpenGL ES. The option that actually works is by definition faster than the one that refuses to execute.
Second, your post suggests that you have an unfortunate, significant, and (sadly) common misunderstanding about how desktop OpenGL works. Textures do not, and never have had a “texture format” of GL_BGRA. What you’re talking about is the pixel transfer format, which describes the format of the data you are passing to OpenGL. It says absolutely nothing about how the texture will store the data. That is defined by the texture’s internal format. And GL_BGRA is not a legal internal format.
FYI: the reason that passing pixel data with GL_BGRA is faster (assuming your internal format is 32-bits-per-pixel, and your data format is 32-bits-per-pixel) is because the driver doesn’t have to flip bits when it transfers data to the internal texture memory. Why would it store things that way? Because Intel chips are little endian, so if you look at a whole 32-bit-per-pixel pixel in BGRA, then turn it around, you get ARGB. Which tends to be the preferred little endian storage for 32-bpp data.
Also, everything I said above applies only to desktop OpenGL. OpenGL ES differs because:
Third, the reason OpenGL ES does it this way is because OpenGL ES wants to minimize the amount of driver-side pixel transfer conversion. Desktop GL implementations have to be able to cope with any pixel data you want. You could use an internal format of GL_R16, while passing pixel data using a format of RGB, encoded as 3/3/2, and the implementation just has to deal with it, culling the G and B channels while expanding the 3-bits-per-red data to 16-bits.
In GL ES, your pixel data’s format and type parameters actually define how OpenGL ES stores the texture. The internal format parameter in this case is irrelevant. Furthermore, ES implementations live in ARM-land, and ARM chips are big endian. There, RGBA is the preferred storage order.
So that’s why it’s done.