SD Card 4-bit Mode License
First of all, some terms.  SDIO refers to an I/O (not memory) card protocol that is based on the SD card protocol.  The STM32F40xxx datasheet says the chip supports 1 and 4-bit SDIO, 1, 4, and 8-bit MMC (MultiMediaCard, and 1 and 4-bit SD cards.

ST Micro most certainly licensed the protocol to design and test the interface, but I doubt very much the SD Card Association would let them make the software protocol available at no cost to anyone who buys their chips, even under an NDA agreement.

I don't see any problem with running the extra wires for the 4-bit mode on your board, and having some sort of jumper options to select between 1 and 4-bit mode.  In fact, I've done exactly that myself.  As far as I know, the proprietary aspect of the 4-bit interface is in the software, not the hardware interface, which is well-0documented.