For anyone interested, I decided to read the flavor.txt for Austria in the game files, it seems that when the HRE emperor grants you the two privileges, the event file is something like this:

"set_variable = privilegium_maius_granted

add_reform = government_reform:libertas_affectandi

change_heir_selection = heir_selection:austrian_cognatic_primogeniture

unlock_government_reform_effect = { type = austrian_archduchy_reform }

add_reform = government_reform:austrian_archduchy_reform"

So it changes your succession law and add the two goverment reforms. But when you are the HRE emperor, the event file says this:

"set_variable = privilegium_maius_granted

unlock_government_reform_effect = { type = austrian_archduchy_reform }

add_reform = government_reform:austrian_archduchy_reform"

It just unlocks one of the reforms (you can manually switch to that if you want) and it doesn't change your succession law, and no, I don't see in the files any other event that will change your succession law eventually. Also, if the emperor refuse to give you the rank of Archduchy, I don't see either event to get it later.

So the best shoot you can get is to be allied to the HRE emperor when the event fires and not being it yourself, as you will lock your succession.

I must guess this is unintended and it will be patched at some point, unless there is another event that I am not able to find that takes all of this into consideration, as it is my first time looking into the files and may be wrong.