As far as the VN goes, Luka is written as a gay guy, who thanks to Japans negative stereotypes surrounding femininity and the like feels that their love for the main character isn't "correct" unless they become a girl, which the D-Mail they send to the past is for.
The translator for Steins;Gate (the official one, so no fantranslation stuff) elaborates on this here:
https://ask.fm/SciADV/answers/134817454903
It's not an unusual situation for this kind of narrative to easily be construed as one that is transgender. Similar situations can be found in Persona 4 with Naoto, whose arc deals with similar notions of gender expectations (although not in a romantic sense) that have been construed by certain people as a transgender narrative.
Is it wrong to consider both of these? For Luka, I quite frankly can't say for sure. The anime (and apparently the dub is the worst offender) did manage to muddle the waters, mainly due to the fact that the anime just has less privy to a character's inner thoughts due to the difference in structure and the dub having a throwaway line about Luka wanting their genitals to match the feelings they hold about Okabe, which wasn't in the Japanese version. Really, for Luka, YMMV + how much you value the literary concept of death of the author when analyzing a work.
For Naoto, it is outright wrong, since it undermines and rewrites fundamental aspects of her character to fit this second read (as well as undermining parts about the concepts of shadow selves and Persona in Persona 4), but this reply isn't that much about her.
Will Hollywood handle this well or not? I quite frankly can't tell. Their track record on tackling these issues isn't great in both directions (Teen Titans GO's live action adaptation can be cited freely as "we tried and misunderstood how to deal with this properly" and there's little effort needed to dig up cases where Hollywood has opted to change a character's sexuality and sometimes gender expression from the source material to avoid offending the type of people that cry about PC culture run amok), but they've been on a better track record as of late soooo... I suggest you stash your pitchforks until we know more.