Does it really matter, though? Even if a creator isn't consciously, actively thinking "I want to insert this theme/subtext," it can still be a part of their underlying way of thinking about the project and its concepts. I've seen it said that often, a writer discovers the theme of a work after it's written. If it's too self-conscious and planned, that isn't necessarily a good thing, because that can make it contrived or forced.
It's not bad if it wasn't in the film.
What I really meant is that I think it's a good thing to think about. I brought it up because I thought it was an interesting connection.
The main reason I think it was missed in the film is because in the Star Trek
universe, ultimately the transporter is safe when operating as intended. McCoy's concerns about having his molecules scrambled are treated as an eccentricity, and the fact that TMP treats them that way is really my exhibit A that the film missed the connection between the transporter and V'Ger.