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The template is just a recommendation for the generator, not a rule of the game.
So, you can attack the guards and walk through the passage without any problems. What is not prohibited is allowed.
I don't see the point in prohibiting passage through glitched passages. This creates problems:
1) identifying a glitched passage (for example, when a lift is located on the border of two respawn areas - this may be a glitched passage or a normal connection of three respawn areas)
2) what to do if the only road leads to this glitched passage.