So according to marqs (the mod board author in the thread at https://shmups.system11.org/viewtopic.php?uid=11668&f=6&t=61285&start=0), there is one difference with the SNES compared to the NES:
“The short scanline actually occurs deeper in vblank”
But it seems odd that this would be the cause of the SNES@60Hz not working on my TV while the NES works perfectly. So I’m still not convinced this is the problem in my case.
Nevertheless, another thought I had regarding the odd/even frames problem… as the OSSC does a bit of buffering already, shouldn’t it be possible for it to buffer just enough to be able to smooth out the odd/even frames into frames with consistent timing? If the OSSC can generate output sync at 2x the pixel clock rate of the NES/SNES PPU, a frame_clocks+2,frame_clocks,frame_clocks+2,… sequence at the input should just equal frame_clocks+1 at the output.
I know this might complicate the FPGA code in order to support just two very quirky systems and may not be top of the priority list for new OSSC firmware. But if possible, it seems like a better alternative than asking people to do yet another complicated hardware mod to their SNES/NES consoles…