I dunno… the joke lands for me, not just the 3PO line, but the idea that the babbling little guy would go out of his way to secretly aid the resistance movement, I think it is meant to be outlandish and comical in the right kind of cheesy way. He doesn’t need to appear again at the end, it has enough of a payoff in and of itself: first we don’t expect this “black market droidsmith” to be a tiny frog fella, then we don’t expect the tiny droidsmith to help out in such a fashion after meeting him. It fits with the idea that good people are willing to stand (and would be even more fitting if the ‘rebellious Kijimi’ ideas are implemented).
I feel nitpicking that one line is just taking things way too serious, the kind of person that would have a legit gripe over this would probably have a problem with just about everything else in this movie. And again it’s a matter of weighing the options and I think it does more harm than good to alter/remove things and cut Jannah’s introduction even shorter for the sake of changing this.