From what I've been seeing around the internet, this problem can't really be solved with my approach.
I am currently writing a program that uses a selection buffer pass over all the objects in the scene. However, one of the objects is a texture in which a large part of it has alpha 0. It works fine when rendering, the alpha values are not displayed, but when in selection mode, the alpha test is skipped, and hovering the mouse over the transparent areas selects the object instead of whatever is behind it.
Is there any way to enable alpha testing in selection mode?