I saw the enderdragon fly through the obsidian towers countless times.
MC-99424
Ender Dragon Glitch - Goes through obsidian.
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I think this is intended, for 2 reaons:
1. simplicity of code. it'd be hard to program it to move around everything
2. abuse. if you made an obsidian cage around where the dragon spawns, it could be abused to 'farm' the final boss of the game. We can't have that, can we?