They block it even when we are neutral or even allied! Why??

I end up having to attack them just to take over those useless single planet gas giant systems. And I can't just raze it, the Academy just re-colonizes all the empty systems.

And also why can't I attack the Academy when I want anyway? When Isyander assings me a role, I have to wait for it to end to declare war... And sometimes he blocks my trade routes 1 turn after I became his vault keeper or something. It's very annoying...

Besides, being unable to attack him at will creates problems for the AI. In my last game, the Academy colonized the only way out from the AI Unfallen's home system, effectively blocking them. The game lasted 230 turns and the Unfallen could not colonize anything at all.

If you take a short look at Public/Diplomacy/DiplomaticRelationStates[Academy].xml, you can find AcademyDiplomaticRelationState(s).

<DiplomaticAbilityChange Operation="Add" DiplomaticAbilityReference="BlockTradingRoutes"/> 

Then you can find this line of xml code. As you can guess from its name, adding that ability blocks trading routes. So, judging by the xml code, it's working as intended for all 3 states, unless devs have written it wrong.

That doesn't make sense though from both design and lore standpoint.

The Academy also blocks trade routes ignoring the trait 'Blockade Breakers' both while allied and not.