Two questions:

1. Why is it so shiny there? 2. Does a chaotic character feel bad only when he enters by the doors, or will he feel bad in the whole area? Also, does it make any difference if he is chaotic, but good?

Answers that are best discovered in-game, mi companero.

There is no way I can find #2 in game...

Need to precise: I can't find the exact answer.

While the door to the chapterhouse makes me roll a saving throw against law and burns my hand only because I'm chaotic, and would burn it more if I was evil, when I'm outside, it just makes me roll a will save (it doesn't tell it is against law or good, and nothing indicates whether the feeling would be worse if I was evil). So my question is: Would New Dunwarren be more "uncomfortable and unnatural" if I was evil? Is it less "uncomfortable and unnatural" because I'm good despite being chaotic?

Also: does the message about how a chaotic / evil char feels in ND trigger after you spend some time there? Because that is what happened right now. Shouldn't it trigger when you enter the area?

IG events have changed what/where in New Dunwarren is/was affecting characters of certain alignments. The messeges, effects, etc. that you receive IG is what you know about what happens to your character.