How to form sentences starting with "it"
It seems to me that you want to use "it" as a Dummy Pronoun (like I have in this sentence). However, you are actually using "it" to refer to "the reason".
Furthermore, I would not use "looks" to describe the intangible noun "reason". A suitable replacement might be "seems" or "feels".
A possible reconstruction (with the substitution) could be:
It seems weird to me that they chose this way.
or
It seems weird to me that they chose this way for the reason that they did.