The thing that changed during the 90's is that mechanical sympathy became optional to achieving a large production. The data input defining the game world was decoupled into assets authored in disconnected ways and "crunched down" to optimized forms - scans, video, digital painting, 3D models. RCT exhibits some of this, too, in that it's using PCM audio samples and prerendered sprites. If the game weren't also a massive agent simulator it would be unremarkable in its era. But even at this time more complex scripting and treating gameplay code as another form of asset was becoming normalized in more genres.
From the POV of getting a desired effect and shipping product, it's irrelevant to engage with mechanical sympathy, but it turns out that it's a thing that players gradually unravel, appreciate and optimize their own play towards if they stick with it and play to competitive extremes, speedrun, mod, etc.
The 64kb FPS QUOD released earlier this year is a good example of what can happen by staying committed to this philosophy even today: the result isn't particularly ambitious as a game design, but it isn't purely a tech demo, nor does it feel entirely arbitrary, nor did it take an outrageous amount of time to make(about one year, according to the dev).
10000x this. Miyamoto starts with a rudimentary prototype and asks himself this. Sadly it seems for many fun is an afterthought they try to patch in somehow.
Texture resolution mismatches causing blurriness/aliasing, floating point errors and bad level design causing collision detection problems (getting stuck in the walls), frame rate and other update rates not being synced causing stutter and lag (and more collision detection problems), bad illumination parameters ruining the look they were going for, numeric overflow breaking everything, bad approximations of constants also breaking everything somewhere eventually, messy model mesh geometry causing glitches in texturing, lighting, animation, collision, etc.
There's probably a lot more I'm not thinking of. They have nothing to do "with the hardware", but the underlying math and logic.
They're also not bugs to "let the programmer figure out". Good programmers and designers work together to solve them. I could just as easily hate on the many criminally ugly, awkward, and plain unfun games made by programmers working alone, but I'll let someone else do that. :)
I remember the early Simpsons video game. Sometimes, due to some bug in it (probably a sign error), you could go through the walls and see the rendered scenery from the other side. It was like you went backstage in a play. It would have made a great Twilight Zone episode!
(But it definitely helps if the game designer knows of the technical limits)
Who formats or cleans up the assets and at least oversees that things are done according to a consistent spec, process, and guidelines? Is that not a game designer or someone under their leadership?
I think in all the cases I gave, what might be completely delegated to "engine design" really should be teamwork with game design and art direction too. This is what the top-level comment was talking about. Even when a game is "well made", they just adopted someone else's standards and that sucks all the soul out of it. This is a common problem in all creative work.
(adding this due to reply depth): Coordination is a big aspect of design and can often be the most impactful to the result.