Hey, sorry for my late answer...
- Well, for the item you say you found doing platforming.. no, it only have a use in the expansion.
-The secret boss area give you the Gazmask earlier in the game
-Some doors you can't interact with !? i"m really lost on this one hmmm
-And yeah the reload while the inventory is open someone else already told me about it but i can't find a way to fix ... It can be exploited to reload safely in fights .. -_-
If you have any other questions dont hesitate!! :) i'll go investigate to see what doors you are talking about.