As far as I'm aware the NES PPU was custom-designed specifically for Famicom/NES products only. There isn't anything else that uses it, so I assume someone at Nintendo thought it'd be cool and that's that.

My real question is: how did Nintendo wind up making the same useless feature twice?

Mode 7 of the SNES PPU has a quirky submode called EXTBG which uses the high bit of each pixel as a priority bit for the sprites. This lets you draw background graphics above sprites in Mode 7 if you so choose. This seems like perfectly ordinary behavior, but the way this is implemented is actually insane.

For context, the SNES PPU-1 implements Mode 7 by individually addressing two 8-bit RAM chips. It has to do this because of memory bandwidth[0] - it puts the tilemap on one chip and the actual pixel data on the other, so it can pipeline the memory reads and just barely fit within the bandwidth limitations of the system. But PPU-2 has a third set of data lines, EXT0-7. When EXTBG is active and the high bit of the pixel is unset, PPU-2 reads color data from EXT0-7 instead of VRAM.

The only reason why this winds up just becoming a priority system, is because Nintendo wired up the second RAM chip's data lines to the EXT0-7 pins, so it reads the same data in either case. But it would work exactly the same as the NES PPU's EXT pins, except the SNES PPU doesn't have a master mode. It is always a "slave"[1] in the terminology of the NES PPU.

In a different world where the EXT pins had been routed to the cartridge port, we could have completely fixed the SNES's biggest limitation: slow DMA. The fastest you can update VRAM is a 2bpp Game Boy sized area of the screen once per frame, or a full-sized area of the screen at 15-30FPS[2]. You'll notice that aligns neatly with the capabilities of the Super Game Boy and Super FX, respectively. Nintendo and other developers got very creative with how they used these chips, but if we had EXT pins on the cartridge bus, that wouldn't have been an issue.

[0] This problem is unique to Mode 7 because, with an affine transform, each pixel requires two unpredictable lookups into a tile map and it's associated tile data. On other modes, the tile can only ever change once per 8 pixels, so less data needs to be read.

[1] God I hate this nomenclature

[2] This is, in fact, a downgrade from the NES. You can actually stream a full picture from VRAM to the PPU and have it change every frame. That's the basis of the trick tom7 uses in the video "Reverse emulating the NES to give it SUPER POWERS!"