For beeing clear, NO, alpha texture baking DO NOT WORK before 3.2
please look at
And see that alpha texture baking DO NOT WORK !
you can bake an object to alpha texture but when you want to bake stacked objects using alpha textures blender writes the (0,0,0,1) color instead of the transparent pixels.
However i noticed big changes ( that i did not test further ) on blender 3.2 that make me say it finally works.
@Marilux_Fiorenzani :
I meant 7 years for blender team to solve this problem 
If you are on windows 10 then you don’t need the ‘hacked-for-making-it-working_on-win7’ blender version. Just go to blender.org and download the later version and install it 
Then you can give a try to the 3.2 awesome baking-to-alpha of alpha objects.
@joseph :
LOL !
You are true but this workaround is just not an option
I guess it’s time for blender to handle properly simple things before it handles serious things
Happy blending !