True, I did not think of the pi/phi distinction when writing this. There are other quirks exclusive to Linear B that don't occur in Linear A though, such as three different ways to write the phoneme "A" with no clear pattern on when is which one used.

With regard to the origin of the script, Linear A documents have been dated to earlier times than Linear B. And then, there is also an even earlier hieroglyphic script, but its relation to Linear A has not been established.