Entering Academy from secret entrance breaks two quests.

[Rupert Giles]

The game gave me no indication that by entering the Academy from the secret entrance was going to ruin these quests. I did not even realize they were broken until many hours later. Too late to load a save. It made quests "Seeking Revenge" and "Familiar Face" unable to complete.

Seeking Revenge: My quest instructs me to find Gareth somewhere on the Nameless Island.
Gareth is found dead by the Elven Temple. The quest does not progress nor complete. Even after talking to his spirit.
Familiar Face: Delorus disappeared completely. The quest does not progress nor complete.
No updates or anything on these quests. After reading about the quests online it appears I will not be able to complete either quest.
Definitive Edition my ass.

[Echsrick]

i think that would even happen if you enter it the main entrance, because the events auto advance on there own, wich makes sense, much like the dalies event at the gate of fort joy auto advances if 1 of your characters escapes the fort

[Chaoslink]

There are certain main objective quests that trigger a "progression of time" that causes certain events to proceed. Since you confront Alexander inside the Academy, there's no reason he'd still be over at the Elven camp. This means that the situation with Garreth proceeds without your intervention.

A similar time advancement happens when you first escape Fort Joy into the swamps. If you do so and didn't progress the event at the gate with Atusa the lizard being killed by Dallis, that event progresses anyway without you. This is noteworthy as many players will level up in the fort enough to confront and fight Dallis right there and get her hammer upon winning the fight.

If you want to avoid these things, you need to avoid progressing the main quest until you've completed the side objectives. Its hard to know that the back entrance is the main quest though.

Nothing to worry though, they're not necessarily essential quests and most of the experience that could be gained by completing them can also be gained either way. You're not really missing much.

[phenir]

I think it's more that you can easily just stumble upon the secret entrance and advance all these quests without warning.

[Echsrick]

does it not only advances if you actualy enter the door that is in the secret dug room? because trying to enter that door promts this "who goin to be divine?" text, instead of using the secret stairs of the cave entrance

[Rupert Giles]

Entering the Academy doesn't even advance the quests. They are still in your log like they still can be completed. It should at least update them so you know that they can't be completed. It would be nice from even a lore standpoint.
A game shouldn't require me to google stuff to find out what's going on within the game.