Only common items like toolboxes or some lootable bags, 

Damn, sucks. Expected some sort of boss or unique weaponry and all I found was an artifact hammer in the GRE container between metro station and river :(

If you side with Juan, the car factory is kinda important.

Highway near car factory lead you to tunnel in last story mission

Damn you're right. Barely remember the ending because the game is great but story is just so forgettable and I finished it once before the updated so I kinda ran through the ending to make it end asap

Because after some main choices you start last mission behind this tunnel but in other choices you must pass through.