I'll make a note to look in some old mags for the Super FX prices, but I really don't remember them being more expensive than Nintendo first party in general. Maybe like $5 more or something. The Super FX was a pretty cheap chip, the 2 is actually the version Argonaut originally made, but Nintendo said it was too costly, so they cut its clocks in half for Star Fox, Stunt Race, etc. It's a really fast, really specific RISC IIRC. Even the RISC CPUs that consoles used are still mostly off-the-shelf, but SuperFX was even more stripping out stuff a game would never use or that was replicated elsewhere in the hardware (sound, hardware to draw the graphics, etc.).
The original SuperFX spec called for 21Mhz which is kinda nuts for a CPU they were putting inside the carts without special cooling. The 486 at the time (1990) was only like 25Mhz. (Also, the SuperFX was originally considered as a NES chip.)
Lots of SNES games used custom chips though, same with NES, to get around that slow CPU. Genesis carts didn't use any except for Virtua Racing. (Which was so expensive that Sega considered just selling a plug-in cartridge that contained the SVP in it and then you'd plug games into that.)
The biggest cost by far in that era was simply the ROM costs. Street Fighters were so expensive as they were always on the high end of the ROM sizes. Which is why Capcom took a bath on Super Street Fighter II, they overproduced demand on 32 megabit carts (40 megabit for the Genesis edition!), the largest of the time, AND ROM/RAM costs shot up in Asia at the same time. Acclaim similarly got smashed on 32 megabit carts.