I think I've done everything, but a few mysteries remain

[decondelite]

I've pretty much beaten everything I could in the game, collected every item (except the Feather Hat that I haven't found), have beaten the [inspoiler]"Makai Four"[/inspoiler], built myself a crapton of S ranked puppets, but there are still a few things that remain mysteries for me.

1) Is the door in the underground of the myouren temple cemetery supposed to be opened at some point?
2) Same goes for the locked door in the SDM's corridors.
3) What are the offering spots and jizous for? We see them a bit everywhere. They're here only for decoration purposes?

I won't count all the scenario related stuff in these mysteries, even if I could say a ton of things regarding this matter.

[Greenmittenz]

I can answer these.

1) The map file and warps for the game already exist but they do not activate. I believe it has been confirmed to be included in the C89 update coming up though.
2) Does not have a warp associated with it at all so it will never open. However it may have been what led to the unused areas in the SDM map. If you look here http://i.imgur.com/9d6lmME.png the three sections on the left and bottom can not be accessed in the game but everything else works. You can see that one door lacks a warp at the bottom and all the others just cycle around between each other. I can also tell you that the event in the tree is a hidden Prismatic Candy and another interesting note is that even though there are 7 programmed trainers in this area there are only 6 actual trainers in the table to assign to them. This may be included at a later date and could potential lead to a post game Flandre fight in the future but for now it is unaccessible and there is no Flandre fight in the trainer table.
3) As for the Jizous and offering spots they do nothing. http://i.imgur.com/TDgm9hK.jpg You can see here that they lack an event associated to them so no function there and for the offering spots http://i.imgur.com/avWNxfP.png the 2xx events are reserved for NPCs and things that only have dialogue and no other more "advanced programming" involved with them. They might have served as locations to gap to if they had originally planned to use the Gen6 fly to any route thing from pokemon.

Also seeing as you mentioned it. The Feather Hat appears to be unimplemented as it does not appear as an item you can pick up on any map and is not in any shop. So unless there is an NPC somewhere that gives it to you that I missed then you cant get it.

[decondelite]

Thanks for your answer.
I really have finished the game 100% then.