If you're willing to trust your hardware, you can theoretically program an SPI Flash chip one bit at a time using two debounced switches. I haven't tried running SPI at sub-kilohertz speeds, much less sub-hertz speeds, and it wouldn't be surprising if that failed to work on some hardware. But you can probably find hardware where it will work. A punched paper tape reader or barcode reader would be a more practical way of programming the Flash than manual toggle switches.
If you have a machine that can boot from floppy, you can use an untrusted system to write the floppy, and then verify the contents of the floppy with a magnetic force microscope or magnetic developer fluid, before booting it.
It isn't obvious why you would trust the hardware, though, if you didn't fabricate it.
