Thanks reinob!

The existance of a plaintext script in the binary was the hint I needed.
Your suggestion didn't work, but at offset 0x00023394 there is

setenv mmcnum 1

And with the limited understanding I have of it, 1 stands for the internal EMMC. So I changed the byte to an ASCII zero.

And it works

U-Boot now picks up the scr file from the first SD partion and boots Leste from there, or shows me the menu when the slider is open.

I attached the file here in case anybody needs it.

Search keywords: U-boot patched N900 SD card SDcard first card did not respond to voltage select change boot order