OP is really interesting and I have lots of thoughts on it, which I’ll ramble about below, but in case you lack the time or inclination for that I will put my conclusion up front:
I think you’re entirely reasonable, and I second the sentiment that’s been expressed here several times, that the deal is the author makes the module they want to make and players can take it or leave it.
Now I don’t know if I would get around to playing your module, personally, because over twenty years on and off playing NWN I’ve discovered that by far my favourite way to engage is to make a character and run them through a series of self-contained, unrelated modules by different authors. The modules themselves don’t share an overarching story, but I get the experience of an overarching story that is simply the story of that character’s adventuring career. There are some great epic saga series on the Vault, but I always ultimately have fun stringing together smaller, less epic modules. I think NWN at its core is just really suited to that picaresque style where the player takes on the role of fantasy Clint Eastwood/Yojimbo/etc.
It is interesting that you mention your module being a smaller, self-contained experience - it sounds like the difference is yours is self-contained to the point where it wouldn’t make sense to have the same character doing this dark and weird cthuloid investigation one day, and hacking their way through hordes of gnolls to rescue a princess the next. That’s entirely fair, although if I do play your module there is a good chance I would use your pregen character and then take that character on to play other random modules like I usually do. I’m at a point where the sheer fun of doing the picaresque sequence outweighs any inconsistency of tone, setting, genre etc between the different modules. In fact I kind of like the inconsistencies.
Along the same lines, if a player is doing what I do and leaning in to the “eclectic module sequence” experience then some of the things which are problems from your point of view may become fantastic moments from theirs. For example, that climactic dragon fight that the player short-circuited because they had an arrow of dragon-slaying? Sure, viewing your module as entirely self-contained, it undermines the experience you’re aiming to create. But for that player it might feel like “oh my god, the arrow of dragon slaying that the old hermit gave me back in the Sword Mountains when I was caught up in that whole business with the dragon cult! I knew I was saving this for a reason!” And then they shoot it and it works and that could be an immensely satisfying moment.
But if you are committed to crafting an experience that has its own tone and style, and is intended to be played alone and siloed off from the rest of the NWN experience, then fair enough. I would be aware that you are pushing at the limits of what NWN is though. It does have a default setting, Forgotten Realms, and all the assumptions that come with that - like elves, gnomes, clerics and sorcerers all rubbing shoulders for example, and the meta level assumption that players get to make their own characters and transport them between modules. I’m not saying this is inherently better - in fact my favourite games of all time are the golden age Final Fantasy games, which give you a predetermined set of characters because that’s integral to what those games are. But NWN is a very different thing.
In a way this is the same as the point about players respecting the author’s vision and taking the module on its own terms. As authors we also need to recognise that NWN itself has a particular vision and like it or not we are going to be constrained to some extent by that.
That said, again, there’s nothing wrong with pushing at those restraints and seeing what unexpected stuff you can make with the toolset, and it sounds like that’s what you’re inspired to do. “Follow your bliss” as they say. So to end up where I began, yeah go for it!