They just believed it was canon that they were a girl, because the fan translators had no choice but use the feminine-gendered word "criança" (child).
But unless they juggled the phrases in a unrealistic and fucked way, like suppressing pronouns sometimes to repetitively use "a criança" and make sure the reader knew they were referring to the WORD and not the actual child, than it would never be translated.
I believe that, as Portuguese stands right now, we cannot have a "properly" losslessly translated Undertale. Elu is treated more as a "third, non-binary gender" instead of a true gender neutral, if that makes sense.
The video is more related how grammatical gender relates to objects rather than people, but I still find it really informative on what grammatical gender is and how it's less tied to real gender than you might expect.