I think the difference is mainly in the hologram reveal.
The first film blurs the line of how 'real' Replicants are, but the film nudges us into the direction of regarding Replicants as sapient beings, albeit emotionally atrophied (we see the Replicants have difficulty processing emotional trauma, like they're glitching in a sense). The second film picks up on this, in that we see K yearning to be human, trying to live a normal life, and other Replicants have their dreams of an uprising, with one of them commenting how they each wished they were the son/daughter (I forget the exact line, it's when K realizes that he isn't Deckard's son). However, Joi does have two key differences from the Replicants in this regard. First, she's the only unit of her kind that we see. We don't have any other Jois to contrast her behaviour with. The second is that the final mention of her in any form is the ad, where the final line is "she tells you what you want to hear." As I said, we and K both want Joi to have a 'soul' and be a fully concious being, and we don't want it to be the case that everything she said and did in the film, including "I love you," was just down to programming, but the ad reminds K and the audience that that very well may be the case. From a narrative standpoint, Joi is arguably there to serve K's character arc, while the Replicants in the first film were arguably distinct from Deckard's.
I don't begrudge the film this though, because like many things in the setting, the story benefits from the ambiguity. Is Deckard human or Replicant? Is Joi concious or just code? Dunno, and the films should never say what IMO. I'd say that Joi does have some distinction from Replicants per the reasons mentioned above, but is still keeping in the theme of what it means to be human, how does one define humanity, the blurred line between human and machine, loneliness and isolation, etc.
Yes we are reminded that she is a mass produced product, but that doesn't exclude her having a "soul" of her own. She's apparently a learning, thinking program, capable of adapting to new situations and circumstances, but she doesn't only tell K what he wanted to hear. There were times where she was clearly pushing his boundaries. Expressing an interest of her own, like how she wanted to be portable so she could "get out of the house once in a while", or how she hired a callgirl without consulting K on what his wishes might be on the matter.
To me, yes, Factory Default JOI, is as you say, just a device, but it seems perfectly reasonable that given the complexity of technology they have at that stage, that after she's turned on, she becomes far more than just a thing that tells you what you want to hear.
I don't want to cite too many examples from the film, due to spoilers, but there were several scenes where she seemed to be acting with a level of agency and autonomy that would bely the idea of just being a Yes Girl, at least one that's been active as long as it's implied she has been with K.
Also, the fact that an advertisement says something, doesn't mean it's true. Since that's been the major theme of both films, just because something was built to these specifications, they are so complex of a creation, that they have grown beyond their specifications, and become "alive", whatever that means in this context. It's the emotional thrust of the original film, that just because they were built for this job, doesn't mean that's all they are. And it's continued with 2049, with K, having his own clear dreams and desires, something that is stated is a common thing among them. In that scene later on when he's talking to another replicant and they say "we all have that same desire." The way he reacts when he learns certain facts, and what they mean for the details of the case. All of it pointing to being More. More Human Than Human as they say.
I dunno, I just don't see any distinction with JOI, based on what we see. Sure, the label on her box says one thing, but the same is true for the replicants, but they are clearly more than just their factory specs. I felt the same was being established with JOI.
Damn I need to watch that film again, it's been a while, and debating it just reminds me how much I love the little things Denis did with it xD