@CortAmmon hit the nail on the head and your answer partly confirms this. This is a story that is being told from a robot's perspective. To whom is the Robot telling the story too? English speaking humans, and thus the robot would construct the story into a language that humans would understand and but the robot would encounter logical inconsistencies with their internal thought process as you point out that the narrator does not comprehend the nature of biological gender and grammatical gender, but English is a language that does have gendered language and infrequently use gendered for nouns that do not have a gender. As a general rule in English Language, the pronoun "It" is read as a dehumanizing proverb when applied to something that is humanized. Even in the generic, "It" is avoided, with either a gender neutral "he", a gender binary "he or she" or "s/he" or even a collective singular they if the generic person is also of a unknown quality. With animals, the generic will be an it. And with animals and humans, when the generic becomes a specific indibidual the generic being will be ascribed proper gendered pronouns. If I was to refer to a generic individual dog, it is a dog. If I were to tell you about a MY dog, She is a dog (if we want to get real technical, she is a canine and a bitch, but not a dog. Dog originally meant an exclusively male canine in the English language but is the excepted term for either gender in a modern setting would be "Dog". Insert joke about "All Men are Dogs" here.).
There are also cases where an inanimate object may be ascribed a gender when it is anthropomorphized or given human characteristics OR in the case of a human showing affection for the object. More often then not in the later case, it is the feminine . One would never refer to the U.S.S. Enterprise by any pronoun other than "She" or you will be punched by both Kirk and Picard (I never felt Archer was an effective fighter to punch someone over the slight, but sure, why not... in theory). And the brooding superhero of the night will tell anyone that he fights the city's inordinate crime problem because "she needs me". Unless the inanimate object is given a voice and speaks with characters, it will almost always be likened to a lady with a mind of her own. However, if the object has male voice and personality, then he may be appropriate. While my car doesn't talk to me and is lovingly called a she, KITT from Night Rider talks to Hasslehauf and is very much a He.
So let's bring this home. Your narrator is from a group of robots who have not encountered the concept of gender, either in the biological sense or grammatical sense, yet are relating their experience in a language that uses both concepts of gender in illogical ways. You should put yourself in the robot's eyes and consider what it would do. Would it assign gender because to the robot, Thomas is a creature with specific personhood and thus, would be rude in English language to call Thomas an "It"? Or would the narrator call Thomas an "it" because Thomas meets the standard definition of a genderless item and thus logically would be an it, even though most of the Narrator's intended audience would cringe (an emotional response to an emotional taboo). Or, would the robot, in confusion of the pronoun troubles it faces, do away with any use of pronouns that where the rules of fuzzy as it introduces and illogical break.
In actual code, pronouns do not exist but there is the concept of objects and pointers. An object is a single collection of like data. An unique object of "bicycle" will have data in common with all bicycles (color, size of wheels, width of handle bars, ect) but those data may not be identical. A pointer is a term used to refer to only one specific instanse of an object in memory at any time. A pointer of bike_1 can be used to a specific bicycle with specific details in memory and will continue to do so until a bike_1 is redefined to mean a different instance of bicycle. So the concept of nouns (specific objects) and pronouns (pointers) is not unfamiliar to a robot. It can make the translation work.
And your assessment of German is wrong. German does not tie individual biological gender to a grammatical gender. For example, the German word for "girl" is gender neutral, but it is not unheard of to use feminine words to describe a specific girl. If I say the phrase "The girl, she is pretty" in German (Das Mädchen (The Girl), sie (she) ist (is) schön (pretty)) you can see I am using the Neutral gendered article "Das" but the feminine third person pronoun "sie" because I am refering to a specific person and not a generic girl. The German word for "Der Robot" is in the generic a robot, but if I was refering to Optimus Prime's um... "girlfriend" for want of a better word, Elita-1 (also a transformer and traditionally uses feminine pronouns) the correct way for saying of Elita-1 "She is the Robot" would be in German "Sie ist der Robot", not "Er (he) is der Robot." Elita-1 is a person using the pronouns she, not he. But she is a robot, which is a grammatical male gender article Der. There is also a recent trend among german speakers to change gramatical genders of words when speaking of an individual who is not of the generic words gender so "Sie ist die Robot" may be used since the robot is identified as a female gramatically already by "she" refering to a specific robot that is a feminine being.
And by the way "Die Bart, Die" is not German for "The Bart, The" as Bart is a male so it would be "Der Bart, Der"...
The best way to handle this is how does the narrating robot want to come off to the humans (as well as you the writer). If the narrator wants humans to think of robots as human like, the narrator might make a change to engender the characters as humans speaking English would be uncomfortable referring to things with personhood with the pronoun "it". If the robot is supposed to come off as logical and cold or alien to humans, the robot will refer to robots with correct grammatical gender "it" as there is nothing wrong with calling things with personhood as "it" when those things with personhood are without capability of gender. It is logical. The final example bot encapsulates the alien nature of robot thinking but the human nature of language confusion and lack or clarity on the rules of grammer. By refusing to ever refer to things with personhood by any pronouns, the robot narrator avoids the question all together, showing humility in that the narrator doesn't have a clear answer to the translation problem and doesn't think in English, but Binary and Computer. But it's also alien to the reader as a native English speaker would use pronouns in this situation. This method shows the narrator as both capable of human qualities (speaking a new language poorly is a human thing and translations often cause unintended meaning to be spoken) and preserves that while human like, they are not fully humans but something that thinks differently. After all, while you correctly discovered that German Language does give all nouns a gender with little rhyme or reason, you incorrectly believed that a word implied gender for all individuals of described by the noun (German grammatically is very similar to English, so order of words is important while Gender can be flexible. In Romance Languages like Spanish, French or Latin, order of the word in a sentence is flexible while the gendered case suffix of the words is very important to understanding who did what and what is being described).