I don't think there is an obligation to do that, but it's very hard for any story with elements meanningful to those who read/play it to avoid sending a message. And if that's the case, care should be taken to avoid sending messages you wouldn't want to be sent.
Agreed- especially in that some messages may be real even if they aren't unintentional. Mass Effect, as a series, repeatedly played the Lovecraftian Horror card in regards to technological advancement- whether it was intended or not, there were regular anti-technology overtures of 'there are some things that mere mortal are not meant to know': this came from the incomprehensible themes of always-evil Reaper tech, the relative rarity of benevolent technologies assisting the plot vis-a-vis the extremely hostile and malevolent technologies most of the plots were built around overcoming, and how the factions and people of note most dedicated to understanding and advancing technology were simultaneously the most prone to abuse it in frequently over-the-top horrifying ways. 'Advanced technology' that factored into the plots almost always came with a blood cost, while mysticism and non-technological elements were often far more important to resolving the conflicts posed by evil technology.
Do I think the ME team set out to craft a deliberate anti-technology message? Probably not- certainly not in the way they repeatedly pounded the 'politicians and rule of law are useless: the military and Men of Action are the effective problem solvers!' drum as a theme. But were there enough overtures that it was one of my less interesting elements of the ME universe? Certainly.
Dragon Age is better in this regards, mostly, thanks to shifting themes between works, but it can still have its own unintended messages and themes. DA2 is an extremely sympathetic take on corruption: not only are most of the cast (including the protagonist) exceptionally corrupt individuals, but this is almost universally cast as a good thing, generally intended to elict sympathy rather than condemnation. When the player and company do it, it's often a selling point- they're just looking out for their own, for their beliefs, it's for the greater good, pretty much the universal costs of corruption. Pay no mind to the costs of corruption- in fact, never bring up them up, or that what they are doing is corrupt in the first place. In the few cases where corruption is intended to be condemned (Sister Petrice, Ser Alrik), it's also so over the top villainy and so explicitly unsanctioned that it's more of a cabal at work than everyday corruption. As far as DA2 was concerned, corruption was cool and completely uncontroversial so long as you weren't being a ****** about it. Somehow, for a developer studio that is quite sensitive to other issues, I doubt this was intentional.
If there's a single Bioware trend of unfortunate implications and messaging, though, it's probably with the companions. If I wanted to raise a child to understand that lying, murdering, and general criminality were bad things and that people who do them routinely should be condemned and brought to justice, not admired and enabled, I would not give them any of the Mass Effect of Dragon Age games.
Bioware treats criminality and even brutality as character spice, something to make the character interesting and appealing in the 'bad boy' way rather than, holy ****, Sten and Samara and Wrex have murdered a bunch of people and it barely gets mentioned or considered once we recruit them. Bioware's emphasis on making sympathetic companion characters almost universally means watering down or outright whitewashing or even ignoring past (and even current) crimes, because criminality is unsympathetic even if the reputation is exciting. So instead of dwelling on what got them that reputation, we get 'character development' that provides context/sympathy/whatever to downplay or mitigate whatever actually caused the reputation. It can get to bizarre extremes with the fanbase that takes to these characters, like the Jack-fan who once insisted that Jack never once harmed an innocent or killed someone unprovoked (because all her past was the woobie victim and self-defense, don'tcha know), but even ongoing acts that would be unacceptable if you knew better are uncontroversial or hand-waved away when it comes to companions. Professional blackmailers? Ah, they cover for the team and we can have faith that they will never do anything bad and that they reign in their organized crime networks from hurting people. Terrorists? Not a crime to their name. Veteran mercenaries and bounty hunters? Never killed anyone who didn't deserve it! (Unless they did, but they regret it so the sympathy for the innocent murder victim makes the rest of it alright.) All kinds of **** not only gets waived when it comes to companions, but is actively partaken: sure, let's help our best buddy by setting out as a kill team to take down person X, who totally deserves it because they're totally bad and no one will care (or we are unaccoutnable). Perjury and covering up war crimes? Anything for a friend!
If there's an unintended message going out from Bioware's cast of companions, it's that murderers and criminals make the best True Companions to be adored and admired, rather than being treated like, you know, murderers and criminals who have committed the crimes they have. Or at least I really, really hope it's an unintended message. It's definitely not the sort of thing I want to see normalized. I'm just saying- the most moral and reasonable people in Mass Effect 2 (and two of the most moral and reasonable people in the entire trilogy) are a terrorist and a war criminal who led a genocide project. Guess which parts of them were (not) treated as flaws within the narrative?