Hi!
This is mainly because when you add 4 normal productivity modules to a machine without other speed bonuses, it just directly reduces the speed down to 40%.
If for example Beaconed assembling machine needs to reach crafting speed 8 with 4 productivity modules, it would need to have crafting speed 20 without the modules.
Adding the fullspeed productivity modules allows to "only increase productivity" of this machine.
They produce and get consumed in pairs to inflate their value - so if you use them in a normal vanilla Assembling machine, you do not get the slowdown of normal productivity modules, but you only get half the productivity bonus.
With modern Factorio I couild put the productivity bonus directly into machine prototypes and remove those modules. In fact I have this almost finished, but there are some caveats and new problems this introduces. (mainly disallowing non-productivity recipes from those machines)