I think a lot of this is due to where the nostalgia is being aimed. The number of pixelly games trying to look like a c64 or Amiga is vanishingly small compared to the number trying to look like an NES, SNES, or Genesis. (Or a PSX or N64.) And they’re mostly trying to make things like early first-party hits, not later third-party games that do crazy techniques. How many 8-bit-looking games sound like a Tim Follin soundtrack?
And of course given that those machines are from a generation that stopped being the new hotness about 30y ago, we have pro pixel artists who have never seen a game through a shitty connection to a TV unless they deliberately sought one out or had obsessively retro gaming parents; they just like making these square mosaics look like things.