It seems like a good idea, but if the custom dungeons give XP or loot that carries over, then it would really break the game. If this ever gets added the devs will probably make all custom items temporary. If someone decided to make a weapon like this:
-custom sword begins here-
Indestructible Elemental Blade
Longsword (One-handed)
Equips to: Main Hand, Off Hand
Martial Weapon Proficiency
Base Damage Rating: -didn't bother to do the math-
Damage: (11-18) 1d8 + 10 Magic
Critical Roll: (25%/22-36) 16-20 / x2
Attack Mod: STR -depends on toon-
->Flaming Burst
->Icy Burst
->Shocking Burst
->Acid Burst
Durability 9999/9999
Custom Material (Hardness: 9999)
-custom sword ends here-
...then that sword is just too powerful, and it would make the official dungeons too easy. If someone sets the quest to award 999,999,999 XP then DDO will be filled with maxed players. The dungeon tool will most likely be just for fun if added to the game, and not affect your character after the dungeon. It's a really good idea and I think it should be added, but still not over-power characters (to ensure fair play).