I always laugh at that statement, "The engineers know best" and then the first thing people do is change everything that the bike came out of the factory with. Seats, bars, grips, foot pegs, tires, windscreens, etc.
The manufacturers do most of their decision to make money.
I don't think those two statements are mutually exclusive. Engineers have to design something like a motorcycle to meet a wide spectrum of consumer, and sometimes they just have to simply use the average rider as a baseline for their design. One reason there's an aftermarket for motorcycle products is to service those riders who aren't quite comfortable with this wide spectrum design.
There's a post on ADV Rider that was cross posted here, about a guy who was essentially whinging about buffeting on the Super Tenere. For him, it was so horrible that he found the bike to be virtually unrideable for long periods. Guys like him are why there's an aftermarket for things like windshields. Whereas I've been riding my 2014 for a decade with a stock windshield, and I've never found buffeting to be a problem at all. Evidently I fit the rider profile for whom the S10 was designed. In fact, I've never changed any of the ergonomics on my S10; seat, screen, pegs, all stock. It doesn't mean I'm right and someone else is wrong; a guy with arms a little shorter than mine may need a set of pullback risers to make his bike comfortable for him, whereas I don't. Engineers have to choose a set of parameters to design within; if you fall outside those parameters, then another set of engineers in the aftermarket can come up with some accommodations.
They also have to design within a certain price point targeted towards the market they're trying to reach. I have no doubt that Yamaha's engineers could design something with as much gosh-wow tech as say, a 1300GS. Which very well might push the price of a Super Tenere into the $20,000 and up range. That might place the S10 beyond the market for which it was intended. One theory I've always had about the Super Ten was that it was targeted for a market that wasn't as big as they'd hoped. It was too expensive for the V-Strom/KLR guys, and too cheap and low tech for the BMW/KTM guys.