None of these arguments make any sense.
Alright, we're off to a good start.
Hygiene and diseases will have to be better addressed at some point and suggestions for adding illness are frequent. Of course making more types of illness wouldn't improve it but you can say the same for the military. Military doesn't work perfectly now so why add more stuff to it like tactics, mounts and such? It would only make the problem worse, right?
Adding tactics and mounts would be expanding the military framework rather than piling more content on top. Unless you're saying that as well as adding waste management, Toady should overhaul the entire infection/syndrome/disease system? Because that would be a big task in itself.
Farming needs to be improved and using manure as fertilizer is the logical way to go.
The problems are bigger than that (can just grow the same plants constantly on the same field with no ill effects, farm yields are too high for how much dwarves eat, and other problems but I won't go into them, there's a myriad of threads on the topic already) and the solution is
not as simple as spreading dwarf muck all over it. And by the way, that would be a serious health risk given how little medical knowledge is around and how often they eat plants raw.
And as addressed by Putnam, there actually is fertiliser anyway, so that's really not the missing piece.
Whether it matters or not in a fantasy simulation can be applied to pretty much everything. Why have elaborate meals with different ingredients and not just "food", for example? Why have soapy baths? Why allow for encrusting with different types of bone?
Because there is a chance those details can matter. The ingredients reflect what's produced in the fort and maybe if you manage to butcher a FB or named creature you would end up having biscuits made of it eaten in the dining room. It tells you something and makes that item special, even if a lot of that time it's stuff you aren't interested in. But being a game there isn't exactly the luxury of picking and choosing what to show. However, I cannot think of any situation where sewage affairs are going to contribute to the story. It just becomes another resource your dwarves waste time hauling around, like money was. Remember how that got taken out for being busywork that didn't add much?
Oh and soapy baths actually do have a purpose, they reduce risk of infection when cleaning wounds.
And your flight simulator example makes no sense either. If it was an airport simulator, it'd make more sense and you bet it would include the daily routine of the pilots and the rest of the staff.
Would it though? At best I can imagine maybe a couple of non-working states like "eating" and "sleeping". All abstract though.
Just take a look into history. During the peak of the pest plague in middle age in some areas nearly 90 % of the population died. Whole areas were exterminated. And the main reason for pest is lack of hygiene. And pest is not the only disease caused by that reason. So I would consider that as major factor for each settlement. Even when there is enough food, drink and no external threat, a fortress can go down when you don't take any measures to keep it clean. Various kind of plagues will spread and likely exterminate it completely unless you install a proper waste/sewer management, bath houses and things like that.
But is having specifically dwarf leavings the only and best way to satisfy cleanliness threats? I would have to say no by a long shot. The only way it would become a problem would be if you were to end up eating or drinking it, and dwarves don't really drink water anyway most of the time, so something would need working out there to actually make it a problem.
If you want health concerns, you probably want the same disease overhaul that Deboche does, so that we get things like colds and the plague and whathaveyou that can spread between individuals rather than needing them to step in magical monster goo.