I solved the "Hit any key to stop autoboot" problem with the mcu sending data to u-boot and stopping the boot process.
Basically, it makes the user type "yun" to stop autoboot if they want to get to the u-boot prompt. It's exactly how tp-link routers work with typing "tpl" to stop autoboot.
It does require an upgrade to u-boot and if that goes wrong you brick the Yun. The only way to recover after that is to desolder the flash and go through the whole process of writing a new image and soldering the chip back on.
I used GitHub - pepe2k/u-boot_mod: U-Boot 1.1.4 modification for routers to create a new bootloader with the typing "yun" option and adding some other features to u-boot like a custom web server upload for new firmware.