The warehouse storing endless items from every play through doesn't sound at all like something that would normally exist in a game. Why would your endgame and quest items be available from the get go at a restart? This is specifically brought up with the blood soul sword. Why did he kill FL to make one, if he already had one in storage?
I don't think the warehouse is a normal part of the game, I think its developer room. The game probably hasn't been replaced yet, and the many looping play throughs are tests to make sure quests work properly, all the endings work properly...bug testing. A "developer room" is a special place that you cannot access through normal game play (without glitches), but developer commands can access. These rooms are used for testing purposes, and for example, might include every item in the game so game testers can test them at will.