The common perception of bechira chofshis is that it is no different than choosing between a chocolate ice cream cone and a vanilla ice cream cone. The world is composed of ruchniyus and gashmiyus mixed together, and you get to choose your flavor. However, this is not the case. Ramchal writes in Derech Hashem (I:4:9 - the same idea is found in other seforim like Nefesh haChaim):
ובכל אלה העניינים לא די מה שקונה האדם בעצמו מעלה ושלמות, אלא שמציאות הבריאה כולה בכללה ובפרטה מתעלה ומשתלם, ובפרט על ידי התורה
When you choose the chocolate ice cream cone over the vanilla one, you are the thing that changes – the ice cream cones are no different than they were before. When you exercise your bechira, aided by talmud Torah, it’s not just you who change, but the world changes as well as a result.
If you have a half-full/half empty glass, whether you say it is half-empty or say it is half-full, in either case it is the same glass. When you exercise your bechira, the glass will be full or empty in response to your choice. Bechira is a function of the tzelem Elokim, which is the creative capacity of mankind. Our mental map is not a construct based on how we view “objective” reality, but reality is a construct which results from our mental map (see Tzidkas haTzadik #90).
Someone who is immersed in Torah and sees the world as filled with ruchniyus is not just seeing our world through rose colored glasses, but that person's world is actually different. R' Chanina ben Dosa could use vinegar in place of oil - that's not a matter of perception, but it's living a different reality. By the same token, a rasha can so immerse him/herself in gashmiyus that even that which is holy and pure is transformed into something unrecognizable to us. They look at Torah and fail to see its beauty and truth not because that beauty and truth is lacking, but because they have chosen to construct a frame of reference which excludes it from their reality.